From b7eea21574abb61ec27e6bcfd773d8338e024bc9 Mon Sep 17 00:00:00 2001 From: Jay Hesselberth Date: Tue, 7 Apr 2026 09:30:49 -0600 Subject: [PATCH] Add missing special tRNA structures (fMet, Ile2, SeC) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The MODOMICS filter in generate_svgs.py used GtRNAdb isotype names (fMet, Ile2, SeC) but MODOMICS uses different names (Ini, Ile, Sec), so these three E. coli tRNAs were silently excluded. Additionally, SeC tRNAs require a dedicated covariance model for correct structural alignment due to their extended variable arm. Changes to generate_svgs.py: - Add ISOTYPE_TO_MODOMICS mapping for GtRNAdb→MODOMICS name translation - Add sec_cm to each organism config - Add split_sec_fasta() to align SeC sequences with TRNAinf-*-SeC.cm New structure files: - Escherichia_coli: tRNA-fMet-CAT, tRNA-Ile2-CAT, tRNA-SeC-TCA - Homo_sapiens: tRNA-SeC-TCA Co-Authored-By: Claude Opus 4.6 (1M context) --- data-raw/structures/generate_svgs.py | 89 ++- .../Escherichia_coli/tRNA-Ala-GGC.json | 156 ++--- .../Escherichia_coli/tRNA-Ala-GGC.svg | 341 +++++----- .../Escherichia_coli/tRNA-Ala-TGC.json | 156 ++--- .../Escherichia_coli/tRNA-Ala-TGC.svg | 341 +++++----- .../Escherichia_coli/tRNA-Arg-ACG.json | 158 ++--- .../Escherichia_coli/tRNA-Arg-ACG.svg | 345 ++++++----- .../Escherichia_coli/tRNA-Arg-CCG.json | 158 ++--- .../Escherichia_coli/tRNA-Arg-CCG.svg | 345 ++++++----- .../Escherichia_coli/tRNA-Arg-CCT.json | 154 ++--- .../Escherichia_coli/tRNA-Arg-CCT.svg | 337 +++++----- .../Escherichia_coli/tRNA-Arg-TCT.json | 158 ++--- .../Escherichia_coli/tRNA-Arg-TCT.svg | 345 ++++++----- .../Escherichia_coli/tRNA-Asn-GTT.json | 156 ++--- .../Escherichia_coli/tRNA-Asn-GTT.svg | 341 +++++----- .../Escherichia_coli/tRNA-Asp-GTC.json | 158 ++--- .../Escherichia_coli/tRNA-Asp-GTC.svg | 345 ++++++----- .../Escherichia_coli/tRNA-Cys-GCA.json | 152 ++--- .../Escherichia_coli/tRNA-Cys-GCA.svg | 333 +++++----- .../Escherichia_coli/tRNA-Gln-CTG.json | 154 ++--- .../Escherichia_coli/tRNA-Gln-CTG.svg | 337 +++++----- .../Escherichia_coli/tRNA-Gln-TTG.json | 154 ++--- .../Escherichia_coli/tRNA-Gln-TTG.svg | 337 +++++----- .../Escherichia_coli/tRNA-Glu-TTC.json | 156 ++--- .../Escherichia_coli/tRNA-Glu-TTC.svg | 341 +++++----- .../Escherichia_coli/tRNA-Gly-CCC.json | 152 ++--- .../Escherichia_coli/tRNA-Gly-CCC.svg | 333 +++++----- .../Escherichia_coli/tRNA-Gly-GCC.json | 156 ++--- .../Escherichia_coli/tRNA-Gly-GCC.svg | 341 +++++----- .../Escherichia_coli/tRNA-Gly-TCC.json | 154 ++--- .../Escherichia_coli/tRNA-Gly-TCC.svg | 337 +++++----- .../Escherichia_coli/tRNA-His-GTG.json | 156 ++--- .../Escherichia_coli/tRNA-His-GTG.svg | 341 +++++----- .../Escherichia_coli/tRNA-Ile-GAT.json | 158 ++--- .../Escherichia_coli/tRNA-Ile-GAT.svg | 345 ++++++----- .../Escherichia_coli/tRNA-Ile2-CAT.json | 466 ++++++++++++++ .../Escherichia_coli/tRNA-Ile2-CAT.svg | 310 ++++++++++ .../Escherichia_coli/tRNA-Leu-CAA.json | 174 +++--- .../Escherichia_coli/tRNA-Leu-CAA.svg | 383 ++++++------ .../Escherichia_coli/tRNA-Leu-CAG.json | 178 +++--- .../Escherichia_coli/tRNA-Leu-CAG.svg | 393 ++++++------ .../Escherichia_coli/tRNA-Leu-GAG.json | 178 +++--- .../Escherichia_coli/tRNA-Leu-GAG.svg | 393 ++++++------ .../Escherichia_coli/tRNA-Leu-TAA.json | 178 +++--- .../Escherichia_coli/tRNA-Leu-TAA.svg | 391 ++++++------ .../Escherichia_coli/tRNA-Leu-TAG.json | 174 +++--- .../Escherichia_coli/tRNA-Leu-TAG.svg | 383 ++++++------ .../Escherichia_coli/tRNA-Lys-TTT.json | 156 ++--- .../Escherichia_coli/tRNA-Lys-TTT.svg | 341 +++++----- .../Escherichia_coli/tRNA-Met-CAT.json | 158 ++--- .../Escherichia_coli/tRNA-Met-CAT.svg | 345 ++++++----- .../Escherichia_coli/tRNA-Phe-GAA.json | 156 ++--- .../Escherichia_coli/tRNA-Phe-GAA.svg | 341 +++++----- .../Escherichia_coli/tRNA-Pro-CGG.json | 158 ++--- .../Escherichia_coli/tRNA-Pro-CGG.svg | 345 ++++++----- .../Escherichia_coli/tRNA-Pro-GGG.json | 158 ++--- .../Escherichia_coli/tRNA-Pro-GGG.svg | 345 ++++++----- .../Escherichia_coli/tRNA-Pro-TGG.json | 158 ++--- .../Escherichia_coli/tRNA-Pro-TGG.svg | 345 ++++++----- .../Escherichia_coli/tRNA-SeC-TCA.json | 580 ++++++++++++++++++ .../Escherichia_coli/tRNA-SeC-TCA.svg | 400 ++++++++++++ .../Escherichia_coli/tRNA-Ser-CGA.json | 184 +++--- .../Escherichia_coli/tRNA-Ser-CGA.svg | 409 ++++++------ .../Escherichia_coli/tRNA-Ser-GCT.json | 190 +++--- .../Escherichia_coli/tRNA-Ser-GCT.svg | 423 +++++++------ .../Escherichia_coli/tRNA-Ser-GGA.json | 180 +++--- .../Escherichia_coli/tRNA-Ser-GGA.svg | 399 ++++++------ .../Escherichia_coli/tRNA-Ser-TGA.json | 180 +++--- .../Escherichia_coli/tRNA-Ser-TGA.svg | 397 ++++++------ .../Escherichia_coli/tRNA-Thr-CGT.json | 156 ++--- .../Escherichia_coli/tRNA-Thr-CGT.svg | 341 +++++----- .../Escherichia_coli/tRNA-Thr-GGT.json | 156 ++--- .../Escherichia_coli/tRNA-Thr-GGT.svg | 341 +++++----- .../Escherichia_coli/tRNA-Thr-TGT.json | 156 ++--- .../Escherichia_coli/tRNA-Thr-TGT.svg | 341 +++++----- .../Escherichia_coli/tRNA-Trp-CCA.json | 156 ++--- .../Escherichia_coli/tRNA-Trp-CCA.svg | 341 +++++----- .../Escherichia_coli/tRNA-Tyr-GTA.json | 174 +++--- .../Escherichia_coli/tRNA-Tyr-GTA.svg | 383 ++++++------ .../Escherichia_coli/tRNA-Val-GAC.json | 158 ++--- .../Escherichia_coli/tRNA-Val-GAC.svg | 345 ++++++----- .../Escherichia_coli/tRNA-Val-TAC.json | 156 ++--- .../Escherichia_coli/tRNA-Val-TAC.svg | 341 +++++----- .../Escherichia_coli/tRNA-fMet-CAT.json | 472 ++++++++++++++ .../Escherichia_coli/tRNA-fMet-CAT.svg | 313 ++++++++++ .../structures/Homo_sapiens/tRNA-Ala-AGC.json | 148 ++--- .../structures/Homo_sapiens/tRNA-Ala-AGC.svg | 325 +++++----- .../structures/Homo_sapiens/tRNA-Ala-CGC.json | 148 ++--- .../structures/Homo_sapiens/tRNA-Ala-CGC.svg | 325 +++++----- .../structures/Homo_sapiens/tRNA-Ala-TGC.json | 148 ++--- .../structures/Homo_sapiens/tRNA-Ala-TGC.svg | 325 +++++----- .../structures/Homo_sapiens/tRNA-Arg-ACG.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Arg-ACG.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Arg-CCG.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Arg-CCG.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Arg-CCT.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Arg-CCT.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Arg-TCG.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Arg-TCG.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Arg-TCT.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Arg-TCT.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Asn-GTT.json | 170 ++--- .../structures/Homo_sapiens/tRNA-Asn-GTT.svg | 345 ++++++----- .../structures/Homo_sapiens/tRNA-Asp-GTC.json | 166 ++--- .../structures/Homo_sapiens/tRNA-Asp-GTC.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-Cys-GCA.json | 166 ++--- .../structures/Homo_sapiens/tRNA-Cys-GCA.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-Gln-CTG.json | 166 ++--- .../structures/Homo_sapiens/tRNA-Gln-CTG.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-Gln-TTG.json | 166 ++--- .../structures/Homo_sapiens/tRNA-Gln-TTG.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-Glu-CTC.json | 166 ++--- .../structures/Homo_sapiens/tRNA-Glu-CTC.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-Glu-TTC.json | 166 ++--- .../structures/Homo_sapiens/tRNA-Glu-TTC.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-Gly-CCC.json | 164 ++--- .../structures/Homo_sapiens/tRNA-Gly-CCC.svg | 333 +++++----- .../structures/Homo_sapiens/tRNA-Gly-GCC.json | 164 ++--- .../structures/Homo_sapiens/tRNA-Gly-GCC.svg | 333 +++++----- .../structures/Homo_sapiens/tRNA-Gly-TCC.json | 166 ++--- .../structures/Homo_sapiens/tRNA-Gly-TCC.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-His-GTG.json | 166 ++--- .../structures/Homo_sapiens/tRNA-His-GTG.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-Ile-AAT.json | 152 ++--- .../structures/Homo_sapiens/tRNA-Ile-AAT.svg | 333 +++++----- .../structures/Homo_sapiens/tRNA-Ile-GAT.json | 152 ++--- .../structures/Homo_sapiens/tRNA-Ile-GAT.svg | 333 +++++----- .../structures/Homo_sapiens/tRNA-Ile-TAT.json | 170 ++--- .../structures/Homo_sapiens/tRNA-Ile-TAT.svg | 345 ++++++----- .../structures/Homo_sapiens/tRNA-Leu-AAG.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Leu-AAG.svg | 371 ++++++----- .../structures/Homo_sapiens/tRNA-Leu-CAA.json | 188 +++--- .../structures/Homo_sapiens/tRNA-Leu-CAA.svg | 389 ++++++------ .../structures/Homo_sapiens/tRNA-Leu-CAG.json | 188 +++--- .../structures/Homo_sapiens/tRNA-Leu-CAG.svg | 389 ++++++------ .../structures/Homo_sapiens/tRNA-Leu-TAA.json | 188 +++--- .../structures/Homo_sapiens/tRNA-Leu-TAA.svg | 389 ++++++------ .../structures/Homo_sapiens/tRNA-Leu-TAG.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Leu-TAG.svg | 371 ++++++----- .../structures/Homo_sapiens/tRNA-Lys-CTT.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Lys-CTT.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Lys-TTT.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Lys-TTT.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Met-CAT.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Met-CAT.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Phe-GAA.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Phe-GAA.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Pro-AGG.json | 166 ++--- .../structures/Homo_sapiens/tRNA-Pro-AGG.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-Pro-CGG.json | 166 ++--- .../structures/Homo_sapiens/tRNA-Pro-CGG.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-Pro-TGG.json | 166 ++--- .../structures/Homo_sapiens/tRNA-Pro-TGG.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-SeC-TCA.json | 550 +++++++++++++++++ .../structures/Homo_sapiens/tRNA-SeC-TCA.svg | 382 ++++++++++++ .../structures/Homo_sapiens/tRNA-Ser-AGA.json | 186 +++--- .../structures/Homo_sapiens/tRNA-Ser-AGA.svg | 385 ++++++------ .../structures/Homo_sapiens/tRNA-Ser-CGA.json | 186 +++--- .../structures/Homo_sapiens/tRNA-Ser-CGA.svg | 385 ++++++------ .../structures/Homo_sapiens/tRNA-Ser-GCT.json | 186 +++--- .../structures/Homo_sapiens/tRNA-Ser-GCT.svg | 385 ++++++------ .../structures/Homo_sapiens/tRNA-Ser-TGA.json | 186 +++--- .../structures/Homo_sapiens/tRNA-Ser-TGA.svg | 385 ++++++------ .../structures/Homo_sapiens/tRNA-Thr-AGT.json | 170 ++--- .../structures/Homo_sapiens/tRNA-Thr-AGT.svg | 345 ++++++----- .../structures/Homo_sapiens/tRNA-Thr-CGT.json | 170 ++--- .../structures/Homo_sapiens/tRNA-Thr-CGT.svg | 345 ++++++----- .../structures/Homo_sapiens/tRNA-Thr-TGT.json | 170 ++--- .../structures/Homo_sapiens/tRNA-Thr-TGT.svg | 345 ++++++----- .../structures/Homo_sapiens/tRNA-Trp-CCA.json | 166 ++--- .../structures/Homo_sapiens/tRNA-Trp-CCA.svg | 337 +++++----- .../structures/Homo_sapiens/tRNA-Tyr-ATA.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Tyr-ATA.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Tyr-GTA.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Tyr-GTA.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Val-AAC.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Val-AAC.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Val-CAC.json | 168 ++--- .../structures/Homo_sapiens/tRNA-Val-CAC.svg | 341 +++++----- .../structures/Homo_sapiens/tRNA-Val-TAC.json | 150 ++--- .../structures/Homo_sapiens/tRNA-Val-TAC.svg | 329 +++++----- .../tRNA-Ala-AGC.json | 150 ++--- .../Saccharomyces_cerevisiae/tRNA-Ala-AGC.svg | 329 +++++----- .../tRNA-Ala-TGC.json | 150 ++--- .../Saccharomyces_cerevisiae/tRNA-Ala-TGC.svg | 329 +++++----- .../tRNA-Arg-ACG.json | 168 ++--- .../Saccharomyces_cerevisiae/tRNA-Arg-ACG.svg | 341 +++++----- .../tRNA-Arg-CCG.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Arg-CCG.svg | 337 +++++----- .../tRNA-Arg-CCT.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Arg-CCT.svg | 337 +++++----- .../tRNA-Arg-TCT.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Arg-TCT.svg | 337 +++++----- .../tRNA-Asn-GTT.json | 170 ++--- .../Saccharomyces_cerevisiae/tRNA-Asn-GTT.svg | 345 ++++++----- .../tRNA-Asp-GTC.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Asp-GTC.svg | 337 +++++----- .../tRNA-Cys-GCA.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Cys-GCA.svg | 337 +++++----- .../tRNA-Glu-CTC.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Glu-CTC.svg | 337 +++++----- .../tRNA-Glu-TTC.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Glu-TTC.svg | 337 +++++----- .../tRNA-Gly-CCC.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Gly-CCC.svg | 337 +++++----- .../tRNA-Gly-GCC.json | 164 ++--- .../Saccharomyces_cerevisiae/tRNA-Gly-GCC.svg | 333 +++++----- .../tRNA-Gly-TCC.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Gly-TCC.svg | 337 +++++----- .../tRNA-His-GTG.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-His-GTG.svg | 337 +++++----- .../tRNA-Ile-AAT.json | 152 ++--- .../Saccharomyces_cerevisiae/tRNA-Ile-AAT.svg | 333 +++++----- .../tRNA-Ile-TAT.json | 168 ++--- .../Saccharomyces_cerevisiae/tRNA-Ile-TAT.svg | 341 +++++----- .../tRNA-Leu-CAA.json | 168 ++--- .../Saccharomyces_cerevisiae/tRNA-Leu-CAA.svg | 371 ++++++----- .../tRNA-Leu-GAG.json | 186 +++--- .../Saccharomyces_cerevisiae/tRNA-Leu-GAG.svg | 383 ++++++------ .../tRNA-Leu-TAA.json | 190 +++--- .../Saccharomyces_cerevisiae/tRNA-Leu-TAA.svg | 393 ++++++------ .../tRNA-Leu-TAG.json | 186 +++--- .../Saccharomyces_cerevisiae/tRNA-Leu-TAG.svg | 383 ++++++------ .../tRNA-Lys-CTT.json | 168 ++--- .../Saccharomyces_cerevisiae/tRNA-Lys-CTT.svg | 341 +++++----- .../tRNA-Lys-TTT.json | 168 ++--- .../Saccharomyces_cerevisiae/tRNA-Lys-TTT.svg | 341 +++++----- .../tRNA-Met-CAT.json | 168 ++--- .../Saccharomyces_cerevisiae/tRNA-Met-CAT.svg | 341 +++++----- .../tRNA-Phe-GAA.json | 168 ++--- .../Saccharomyces_cerevisiae/tRNA-Phe-GAA.svg | 341 +++++----- .../tRNA-Pro-AGG.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Pro-AGG.svg | 337 +++++----- .../tRNA-Pro-TGG.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Pro-TGG.svg | 337 +++++----- .../tRNA-Ser-AGA.json | 186 +++--- .../Saccharomyces_cerevisiae/tRNA-Ser-AGA.svg | 385 ++++++------ .../tRNA-Ser-CGA.json | 186 +++--- .../Saccharomyces_cerevisiae/tRNA-Ser-CGA.svg | 385 ++++++------ .../tRNA-Ser-TGA.json | 186 +++--- .../Saccharomyces_cerevisiae/tRNA-Ser-TGA.svg | 385 ++++++------ .../tRNA-Thr-AGT.json | 168 ++--- .../Saccharomyces_cerevisiae/tRNA-Thr-AGT.svg | 341 +++++----- .../tRNA-Thr-CGT.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Thr-CGT.svg | 337 +++++----- .../tRNA-Thr-TGT.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Thr-TGT.svg | 337 +++++----- .../tRNA-Trp-CCA.json | 166 ++--- .../Saccharomyces_cerevisiae/tRNA-Trp-CCA.svg | 337 +++++----- .../tRNA-Tyr-GTA.json | 172 +++--- .../Saccharomyces_cerevisiae/tRNA-Tyr-GTA.svg | 349 ++++++----- .../tRNA-Val-AAC.json | 170 ++--- .../Saccharomyces_cerevisiae/tRNA-Val-AAC.svg | 345 ++++++----- .../tRNA-Val-CAC.json | 168 ++--- .../Saccharomyces_cerevisiae/tRNA-Val-CAC.svg | 341 +++++----- .../tRNA-Val-TAC.json | 170 ++--- .../Saccharomyces_cerevisiae/tRNA-Val-TAC.svg | 345 ++++++----- .../structures/T4_phage/tRNA-Arg-TCT.json | 154 ++--- .../structures/T4_phage/tRNA-Arg-TCT.svg | 337 +++++----- .../structures/T4_phage/tRNA-Gln-TTG.json | 156 ++--- .../structures/T4_phage/tRNA-Gln-TTG.svg | 341 +++++----- .../structures/T4_phage/tRNA-Gly-TCC.json | 152 ++--- .../structures/T4_phage/tRNA-Gly-TCC.svg | 333 +++++----- .../structures/T4_phage/tRNA-Ile2-CAT.json | 158 ++--- .../structures/T4_phage/tRNA-Ile2-CAT.svg | 345 ++++++----- .../structures/T4_phage/tRNA-Leu-TAA.json | 178 +++--- .../structures/T4_phage/tRNA-Leu-TAA.svg | 391 ++++++------ .../structures/T4_phage/tRNA-Pro-TGG.json | 160 ++--- .../structures/T4_phage/tRNA-Pro-TGG.svg | 349 ++++++----- .../structures/T4_phage/tRNA-Ser-TGA.json | 184 +++--- .../structures/T4_phage/tRNA-Ser-TGA.svg | 409 ++++++------ .../structures/T4_phage/tRNA-Thr-TGT.json | 156 ++--- .../structures/T4_phage/tRNA-Thr-TGT.svg | 341 +++++----- 273 files changed, 38063 insertions(+), 33591 deletions(-) create mode 100644 inst/extdata/structures/Escherichia_coli/tRNA-Ile2-CAT.json create mode 100644 inst/extdata/structures/Escherichia_coli/tRNA-Ile2-CAT.svg create mode 100644 inst/extdata/structures/Escherichia_coli/tRNA-SeC-TCA.json create mode 100644 inst/extdata/structures/Escherichia_coli/tRNA-SeC-TCA.svg create mode 100644 inst/extdata/structures/Escherichia_coli/tRNA-fMet-CAT.json create mode 100644 inst/extdata/structures/Escherichia_coli/tRNA-fMet-CAT.svg create mode 100644 inst/extdata/structures/Homo_sapiens/tRNA-SeC-TCA.json create mode 100644 inst/extdata/structures/Homo_sapiens/tRNA-SeC-TCA.svg diff --git a/data-raw/structures/generate_svgs.py b/data-raw/structures/generate_svgs.py index 60afd216..2447d798 100644 --- a/data-raw/structures/generate_svgs.py +++ b/data-raw/structures/generate_svgs.py @@ -38,21 +38,32 @@ "Escherichia_coli": { "fasta": FASTA_DIR / "eschColi_K_12_MG1655-mature-tRNAs.fa", "cm": CM_DIR / "TRNAinf-bact.cm", + "sec_cm": CM_DIR / "TRNAinf-bact-SeC.cm", }, "Saccharomyces_cerevisiae": { "fasta": FASTA_DIR / "sacCer3-mature-tRNAs.fa", "cm": CM_DIR / "TRNAinf-euk.cm", + "sec_cm": CM_DIR / "TRNAinf-euk-SeC.cm", }, "Homo_sapiens": { "fasta": FASTA_DIR / "hg38-mature-tRNAs.fa", "cm": CM_DIR / "TRNAinf-euk.cm", + "sec_cm": CM_DIR / "TRNAinf-euk-SeC.cm", }, "T4_phage": { "fasta": FASTA_DIR / "phageT4-tRNAs.fa", "cm": CM_DIR / "TRNAinf-bact.cm", + "sec_cm": CM_DIR / "TRNAinf-bact-SeC.cm", }, } +# Map GtRNAdb isotype names to MODOMICS subtype names +ISOTYPE_TO_MODOMICS = { + "fMet": "Ini", + "Ile2": "Ile", + "SeC": "Sec", +} + def main(): """Generate SVGs for all configured organisms.""" @@ -64,21 +75,37 @@ def main(): org_dir = OUTPUT_DIR / org_name org_dir.mkdir(parents=True, exist_ok=True) - # Step 1: Align sequences against tRNAscan-SE CM + # Step 1: Split FASTA into standard and SeC sequences fasta_path = org_info["fasta"] if not fasta_path.exists(): print(f" WARNING: FASTA not found: {fasta_path}") continue + std_fasta, sec_fasta = split_sec_fasta(fasta_path) + + # Step 2a: Align standard sequences against tRNAscan-SE CM cm_path = org_info["cm"] - sto_path = run_cmalign(fasta_path, cm_path) + sto_path = run_cmalign(std_fasta, cm_path) if sto_path is None: print(f" WARNING: cmalign failed for {org_name}") continue - # Step 2: Parse aligned sequences and structures trnas = parse_cmalign_stockholm(sto_path) + # Step 2b: Align SeC sequences with the SeC-specific CM + if sec_fasta is not None: + sec_cm = org_info.get("sec_cm") + if sec_cm and sec_cm.exists(): + sec_sto = run_cmalign(sec_fasta, sec_cm) + if sec_sto is not None: + sec_trnas = parse_cmalign_stockholm(sec_sto) + trnas.update(sec_trnas) + print(f" Added {len(sec_trnas)} SeC tRNA(s)") + else: + print(" WARNING: cmalign failed for SeC sequences") + else: + print(" WARNING: SeC CM not found, skipping SeC tRNAs") + if not trnas: print(f" WARNING: No tRNA data extracted for {org_name}") continue @@ -97,7 +124,10 @@ def main(): filtered = { k: v for k, v in trnas.items() - if extract_isotype(k) in modomics_isotypes + if ISOTYPE_TO_MODOMICS.get( + extract_isotype(k), extract_isotype(k) + ) + in modomics_isotypes } print( f" Filtered to {len(filtered)}/{len(trnas)} tRNAs " @@ -185,6 +215,57 @@ def run_cmalign(fasta_path: Path, cm_path: Path) -> Path | None: return None +def split_sec_fasta(fasta_path: Path) -> tuple[Path, Path | None]: + """Split a FASTA into standard and selenocysteine tRNA sequences. + + SeC tRNAs need a different covariance model for structural alignment. + Returns (standard_fasta_path, sec_fasta_path_or_None). + """ + std_records = [] + sec_records = [] + + with open(fasta_path) as f: + header = None + seq_lines = [] + for line in f: + line = line.rstrip() + if line.startswith(">"): + if header is not None: + record = header + "\n" + "\n".join(seq_lines) + "\n" + if "tRNA-SeC-" in header or "tRNA-Sec-" in header: + sec_records.append(record) + else: + std_records.append(record) + header = line + seq_lines = [] + else: + seq_lines.append(line) + if header is not None: + record = header + "\n" + "\n".join(seq_lines) + "\n" + if "tRNA-SeC-" in header or "tRNA-Sec-" in header: + sec_records.append(record) + else: + std_records.append(record) + + # Write standard sequences to temp file + std_fd, std_path = tempfile.mkstemp(suffix=".fa") + with open(std_path, "w") as f: + f.writelines(std_records) + std_path = Path(std_path) + + # Write SeC sequences if any + sec_path = None + if sec_records: + sec_fd, sec_path = tempfile.mkstemp(suffix=".fa") + with open(sec_path, "w") as f: + f.writelines(sec_records) + sec_path = Path(sec_path) + print(f" Split FASTA: {len(std_records)} standard, " + f"{len(sec_records)} SeC sequences") + + return std_path, sec_path + + def parse_cmalign_stockholm(sto_path: Path) -> dict: """Parse cmalign Stockholm output into per-tRNA sequences and structures. diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Ala-GGC.json b/inst/extdata/structures/Escherichia_coli/tRNA-Ala-GGC.json index 80665623..412723d9 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Ala-GGC.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Ala-GGC.json @@ -3,464 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 71.51, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "G", "x": 71.51, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 71.51, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 71.72, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "U", "x": 71.72, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "A", "x": 71.92, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 64.29, - "y": 106.05, + "y": 98.49, "pos": 8 }, { "base": "A", "x": 58.32, - "y": 110.42, + "y": 102.86, "pos": 9 }, { "base": "G", "x": 54.12, - "y": 116.96, + "y": 109.4, "pos": 10 }, { "base": "C", "x": 46.77, - "y": 116.96, + "y": 109.4, "pos": 11 }, { "base": "U", "x": 39.21, - "y": 116.96, + "y": 109.4, "pos": 12 }, { "base": "C", "x": 31.65, - "y": 116.96, + "y": 109.4, "pos": 13 }, { "base": "A", "x": 26.52, - "y": 111.61, + "y": 104.05, "pos": 14 }, { "base": "G", "x": 18.69, - "y": 110.13, + "y": 102.57, "pos": 15 }, { "base": "C", "x": 11.91, - "y": 113.02, + "y": 105.46, "pos": 16 }, { "base": "U", "x": 7.71, - "y": 119.3, + "y": 111.74, "pos": 17 }, { "base": "G", "x": 7.5, - "y": 126.86, + "y": 119.3, "pos": 18 }, { "base": "G", "x": 11.7, - "y": 133.15, + "y": 125.59, "pos": 19 }, { "base": "G", "x": 18.69, - "y": 136.03, + "y": 128.47, "pos": 20 }, { "base": "A", "x": 26.52, - "y": 134.55, + "y": 126.99, "pos": 21 }, { "base": "G", "x": 31.44, - "y": 129.2, + "y": 121.64, "pos": 22 }, { "base": "A", "x": 39.42, - "y": 129.2, + "y": 121.64, "pos": 23 }, { "base": "G", "x": 46.56, - "y": 129.2, + "y": 121.64, "pos": 24 }, { "base": "C", "x": 54.33, - "y": 129.2, + "y": 121.64, "pos": 25 }, { "base": "G", "x": 58.33, - "y": 135.48, + "y": 127.92, "pos": 26 }, { "base": "C", "x": 64.83, - "y": 139.67, + "y": 132.11, "pos": 27 }, { "base": "U", "x": 64.83, - "y": 147.23, + "y": 139.67, "pos": 28 }, { "base": "U", "x": 64.83, - "y": 154.79, + "y": 147.23, "pos": 29 }, { "base": "G", "x": 64.62, - "y": 162.35, + "y": 154.79, "pos": 30 }, { "base": "C", "x": 64.83, - "y": 169.91, + "y": 162.35, "pos": 31 }, { "base": "A", "x": 60.15, - "y": 175.68, + "y": 168.12, "pos": 32 }, { "base": "U", "x": 59.54, - "y": 183.23, + "y": 175.67, "pos": 33 }, { "base": "G", "x": 63.58, - "y": 189.49, + "y": 181.93, "pos": 34 }, { "base": "G", "x": 70.74, - "y": 191.9, + "y": 184.34, "pos": 35 }, { "base": "C", "x": 78.12, - "y": 189.49, + "y": 181.93, "pos": 36 }, { "base": "A", "x": 82.57, - "y": 183.23, + "y": 175.67, "pos": 37 }, { "base": "U", "x": 81.96, - "y": 175.68, + "y": 168.12, "pos": 38 }, { "base": "G", "x": 76.86, - "y": 169.91, + "y": 162.35, "pos": 39 }, { "base": "C", "x": 77.07, - "y": 162.35, + "y": 154.79, "pos": 40 }, { "base": "A", "x": 77.28, - "y": 154.79, + "y": 147.23, "pos": 41 }, { "base": "A", "x": 77.28, - "y": 147.23, + "y": 139.67, "pos": 42 }, { "base": "G", "x": 76.86, - "y": 139.67, + "y": 132.11, "pos": 43 }, { "base": "A", "x": 83.08, - "y": 144.52, + "y": 136.96, "pos": 44 }, { "base": "G", "x": 90.22, - "y": 144.77, + "y": 137.21, "pos": 45 }, { "base": "G", "x": 96.34, - "y": 140.33, + "y": 132.77, "pos": 46 }, { "base": "U", "x": 98.65, - "y": 133.07, + "y": 125.51, "pos": 47 }, { "base": "C", "x": 95.85, - "y": 126.05, + "y": 118.49, "pos": 48 }, { "base": "A", "x": 89.53, - "y": 122.23, + "y": 114.67, "pos": 49 }, { "base": "G", "x": 96.67, - "y": 122.23, + "y": 114.67, "pos": 50 }, { "base": "C", "x": 104.44, - "y": 122.23, + "y": 114.67, "pos": 51 }, { "base": "G", "x": 111.79, - "y": 122.23, + "y": 114.67, "pos": 52 }, { "base": "G", "x": 119.35, - "y": 122.23, + "y": 114.67, "pos": 53 }, { "base": "U", "x": 125.33, - "y": 127.12, + "y": 119.56, "pos": 54 }, { "base": "U", "x": 132.88, - "y": 127.52, + "y": 119.96, "pos": 55 }, { "base": "C", "x": 139.13, - "y": 123.28, + "y": 115.72, "pos": 56 }, { "base": "G", "x": 141.33, - "y": 116.11, + "y": 108.55, "pos": 57 }, { "base": "A", "x": 139.34, - "y": 108.95, + "y": 101.39, "pos": 58 }, { "base": "U", "x": 132.88, - "y": 104.7, + "y": 97.14, "pos": 59 }, { "base": "C", "x": 125.33, - "y": 105.1, + "y": 97.54, "pos": 60 }, { "base": "C", "x": 119.56, - "y": 109.99, + "y": 102.43, "pos": 61 }, { "base": "C", "x": 112.0, - "y": 109.99, + "y": 102.43, "pos": 62 }, { "base": "G", "x": 104.23, - "y": 109.99, + "y": 102.43, "pos": 63 }, { "base": "C", "x": 96.88, - "y": 109.99, + "y": 102.43, "pos": 64 }, { "base": "U", "x": 89.32, - "y": 109.99, + "y": 102.43, "pos": 65 }, { "base": "U", "x": 83.96, - "y": 104.66, + "y": 97.1, "pos": 66 }, { "base": "A", "x": 84.16, - "y": 97.1, + "y": 89.54, "pos": 67 }, { "base": "G", "x": 83.75, - "y": 89.54, + "y": 81.98, "pos": 68 }, { "base": "C", "x": 83.96, - "y": 81.98, + "y": 74.42, "pos": 69 }, { "base": "U", "x": 83.96, - "y": 74.42, + "y": 66.86, "pos": 70 }, { "base": "C", "x": 83.96, - "y": 66.86, + "y": 59.3, "pos": 71 }, { "base": "C", "x": 83.96, - "y": 59.3, + "y": 51.74, "pos": 72 }, { "base": "A", "x": 84.16, - "y": 51.74, + "y": 44.18, "pos": 73 }, { "base": "C", "x": 83.96, - "y": 44.18, + "y": 36.62, "pos": 74 }, { "base": "C", "x": 83.96, - "y": 36.62, + "y": 29.06, "pos": 75 }, { "base": "A", "x": 84.16, - "y": 29.06, + "y": 21.5, "pos": 76 } ], "width": 154.67, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Ala-GGC", "sequence": "GGGGCUAUAGCUCAGCUGGGAGAGCGCUUGCAUGGCAUGCAAGAGGUCAGCGGUUCGAUCCCGCUUAGCUCCACCA", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Ala-GGC.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Ala-GGC.svg index 6f73eeff..4243b98d 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Ala-GGC.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Ala-GGC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Ala-GGC + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 L 99.5865 103.915 "/> + d="M 107.146 107.803 L 107.146 103.915 "/> + d="M 114.706 107.803 L 114.706 103.915 "/> - - - G - - - G + d="M 122.266 107.803 L 122.266 103.915 "/> + + G - - G + + G - - G + + G - - C + + G - - U + + C - - A + + U - - U + + A - - A + + U - - G + + A - - C + + G - - U + + C - - C + + U - - A + + C - - G + + A - - C + + G - - U + + C - - G + + U - - G + + G - - G + + G - - A + + G - - G + + A - - A + + G - - G + + A - - C + + G - - G + + C - - C + + G - - U + + C - - U + + U - - G + + U - - C + + G - - A + + C - - U + + A - - G + + U - - G + + G - - C + + G - - A + + C - - U + + A - - G + + U - - C + + G - - A + + C - - A + + A - - G + + A - - A + + G - - G + + A - - G + + G - - U + + G - - C + + U - - A + + C - - G + + A - - C + + G - - G + + C - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - U + + A - - C + + U - - C + + C - - C + + C - - G + + C - - C + + G - - U + + C - - U + + U - - A + + U - - G + + A - - C + + G - - U + + C - - C + + U - - C + + C - - A + + C - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Ala-TGC.json b/inst/extdata/structures/Escherichia_coli/tRNA-Ala-TGC.json index c015e6f2..128e8d72 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Ala-TGC.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Ala-TGC.json @@ -3,464 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": 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"base": "C", "x": 87.02, - "y": 44.18, + "y": 36.62, "pos": 75 }, { "base": "C", "x": 87.02, - "y": 36.62, + "y": 29.06, "pos": 76 }, { "base": "A", "x": 87.22, - "y": 29.06, + "y": 21.5, "pos": 77 } ], "width": 157.73, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Arg-TCT", "sequence": "GCGCCCUUAGCUCAGUUGGAUAGAGCAACGACCUUCUAAGUCGUGGGCCGCAGGUUCGAAUCCUGCAGGGCGCGCCA", "structure": "<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Arg-TCT.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Arg-TCT.svg index c45d3e33..aedbce68 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Arg-TCT.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Arg-TCT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Arg-TCT + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,260 +60,254 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 95.0847 107.803 L 95.0847 103.915 "/> + d="M 102.645 107.803 L 102.645 103.915 "/> + d="M 110.205 107.803 L 110.205 103.915 "/> + d="M 117.765 107.803 L 117.765 103.915 "/> - - - G - - - C + d="M 125.325 107.803 L 125.325 103.915 "/> + + G - - G + + C - - C + + G - - C + + C - - C + + C - - U + + C - - U + + U - - A + + U - - G + + A - - C + + G - - U + + C - - C + + U - - A + + C - - G + + A - - U + + G - - U + + U - - G + + U - - G + + G - - A + + G - - U + + A - - A + + U - - G + + A - - A + + G - - G + + A - - C + + G - - A + + C - - A + + A - - C + + A - - G + + C - - A + + G - - C + + A - - C + + C - - U + + C - - U + + U - - C + + U - - U + + C - - A + + U - - A + + A - - G + + A - - U + + G - - C + + U - - G + + C - - U + + G - - G + + U - - G + + G - - G + + G - - C + + G - - C + + C - - G + + C - - C + + G - - A + + C - - G + + A - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - A + + A - - U + + A - - C + + U - - C + + C - - U + + C - - G + + U - - C + + G - - A + + C - - G + + A - - G + + G - - G + + G - - C + + G - - G + + C - - C + + G - - G + + C - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 45.4847 A 1.78191,1.78191 270 0,0 75.7018,43.7028L 72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Asn-GTT.json b/inst/extdata/structures/Escherichia_coli/tRNA-Asn-GTT.json index cc4b51d4..b8c4c973 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Asn-GTT.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Asn-GTT.json @@ -3,464 +3,464 @@ { "base": "U", "x": 71.72, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 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tRNA-Asp-GTC + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,260 +60,254 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 95.0847 107.803 L 95.0847 103.915 "/> + d="M 102.645 107.803 L 102.645 103.915 "/> + d="M 110.205 107.803 L 110.205 103.915 "/> + d="M 117.765 107.803 L 117.765 103.915 "/> - - - G - - - G + d="M 125.325 107.803 L 125.325 103.915 "/> + + G - - A + + G - - G + + A - - C + + G - - G + + C - - G + + G - - U + + G - - A + + U - - G + + A - - U + + G - - U + + U - - C + + U - - A + + C - - G + + A - - U + + G - - C + + U - - G + + C - - G + + G - - U + + G - - U + + U - - A + + U - - G + + A - - A + + G - - A + + A - - U + + A - - A + + U - - C + + A - - C + + C - - U + + C - - G + + U - - C + + G - - C + + C - - U + + C - - G 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"A", "x": 82.21, - "y": 29.06, + "y": 21.5, "pos": 74 } ], "width": 152.71, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Cys-GCA", "sequence": "GGCGCGUUAACAAAGCGGUUAUGUAGCGGAUUGCAAAUCCGUCUAGUCCGGUUCGACUCCGGAACGCGCCUCCA", "structure": "<<<<<<<..<<<<.......>>>>.<<<<<.......>>>>>....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Cys-GCA.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Cys-GCA.svg index 98131d57..6589cac6 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Cys-GCA.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Cys-GCA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="152.713" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Cys-GCA + @@ -30,19 +33,19 @@ d="M 76.6454 94.4085 L 80.5334 94.4085 "/> + d="M 55.0824 110.885 L 55.0824 114.773 "/> + d="M 47.5224 110.885 L 47.5224 114.773 "/> + d="M 39.9624 110.885 L 39.9624 114.773 "/> + d="M 32.4024 110.885 L 32.4024 114.773 "/> + d="M 69.7584 129.42 L 73.6464 129.42 "/> @@ -57,251 +60,245 @@ d="M 69.7584 159.66 L 73.6464 159.66 "/> + d="M 90.0703 107.803 L 90.0703 103.915 "/> + d="M 97.6303 107.803 L 97.6303 103.915 "/> + d="M 105.19 107.803 L 105.19 103.915 "/> + d="M 112.75 107.803 L 112.75 103.915 "/> - - - G - - - G + d="M 120.31 107.803 L 120.31 103.915 "/> + + G - - C + + G - - G + + C - - C + + G - - G + + C - - U + + G - - U + + U - - A + + U - - A + + A - - C + + A - - A + + C - - A + + A - - A + + A - - G + + A - - C + + G - - G + + C - - G + + G - - U + + G - - U + + U - - A + + U - - U + + A - - G + + U - - U + + G - - A + + U - - G + + A - - C + + G - - G + + C - - G + + G - - A + + G - - U + + A - - U + + U - - G + + U - - C + + G - - A + + C - - A + + A - - A + + A - - U + + A - - C + + U - - C + + C - - G + + C - - U + + G - - C + + U - - U + + C - - A + + U - - G + + A - - U + + G - - C + + U - - C + + C - - G + + C - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - C + + A - - U + + C - - C + + U - - C + + C - - G + + C - - G + + G - - A + + G - - A + + A - - C + + A - - G + + C - - C + + G - - G + + C - - C + + G - - C + + C - - U + + C - - C + + U - - C + + C - - A + + C - - A + + A - - 5' + d="M 72.4694 45.4847 A 1.78191,1.78191 270 0,0 70.6875,43.7028L 67.1236 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Gln-CTG.json b/inst/extdata/structures/Escherichia_coli/tRNA-Gln-CTG.json index c76eac9e..d4aaea5c 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Gln-CTG.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Gln-CTG.json @@ -3,458 +3,458 @@ { "base": "U", "x": 69.76, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 69.55, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "G", "x": 69.55, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 69.55, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": 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"tRNA-Gln-CTG", "sequence": "UGGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA", "structure": "<<<<<<<..<<<<.......>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Gln-CTG.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Gln-CTG.svg index 65a1cf34..eb519bde 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Gln-CTG.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Gln-CTG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="152.713" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Gln-CTG + @@ -30,19 +33,19 @@ d="M 76.6454 94.4085 L 80.5334 94.4085 "/> + d="M 55.0824 110.885 L 55.0824 114.773 "/> + d="M 47.5224 110.885 L 47.5224 114.773 "/> + d="M 39.9624 110.885 L 39.9624 114.773 "/> + d="M 32.4024 110.885 L 32.4024 114.773 "/> + d="M 69.7584 129.42 L 73.6464 129.42 "/> @@ -57,254 +60,248 @@ d="M 69.7584 159.66 L 73.6464 159.66 "/> + d="M 90.0703 107.803 L 90.0703 103.915 "/> + d="M 97.6303 107.803 L 97.6303 103.915 "/> + d="M 105.19 107.803 L 105.19 103.915 "/> + d="M 112.75 107.803 L 112.75 103.915 "/> - - - U - - - G + d="M 120.31 107.803 L 120.31 103.915 "/> + + U - - G + + G - - G + + G - - G + + G - - U + + G - - A + + U - - U + + A - - C + + U - - G + + C - - C + + G - - C + + C - - A + + C - - A + + A - - G + + A - - C + + G - - G + + C - - G + + G - - U + + G - - A + + U - - A + + A - - G + + A - - G + + G - - C + + G - - A + + C - - C + + A - - C + + C - - G + + C - - G + + G - - A + + G - - U + + A - - U + + U - - C + + U - - U + + C - - G + + U - - A + + G - - U + + A - - U + + U - - C + + U - - C + + C - - G + + C - - G + + G - - C + + G - - A + + C - - U + + A - - U + + U - - C + + U - - C + + C - - G + + C - - A + + G - - G + + A - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - A + + A - - U + + A - - C + + U - - C + + C 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"<<<<<<<..<<<<.......>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Gln-TTG.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Gln-TTG.svg index 704d8636..c1ba8fe6 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Gln-TTG.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Gln-TTG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="152.713" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Gln-TTG + @@ -30,19 +33,19 @@ d="M 76.6454 94.4085 L 80.5334 94.4085 "/> + d="M 55.0824 110.885 L 55.0824 114.773 "/> + d="M 47.5224 110.885 L 47.5224 114.773 "/> + d="M 39.9624 110.885 L 39.9624 114.773 "/> + d="M 32.4024 110.885 L 32.4024 114.773 "/> + d="M 69.7584 129.42 L 73.6464 129.42 "/> @@ -57,254 +60,248 @@ d="M 69.7584 159.66 L 73.6464 159.66 "/> + d="M 90.0703 107.803 L 90.0703 103.915 "/> + d="M 97.6303 107.803 L 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- G + + A - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 72.4694 45.4847 A 1.78191,1.78191 270 0,0 70.6875,43.7028L 67.1236 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Glu-TTC.json b/inst/extdata/structures/Escherichia_coli/tRNA-Glu-TTC.json index 0fccaf00..d22790cb 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Glu-TTC.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Glu-TTC.json @@ -3,464 +3,464 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "U", "x": 74.78, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 74.78, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "C", "x": 74.78, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 74.78, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "C", "x": 74.78, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "U", "x": 74.78, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 67.34, - "y": 106.05, + "y": 98.49, 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"<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Glu-TTC.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Glu-TTC.svg index 6a917265..9bc33232 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Glu-TTC.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Glu-TTC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Glu-TTC + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,257 +60,251 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 95.0847 107.803 L 95.0847 103.915 "/> + d="M 102.645 107.803 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a/inst/extdata/structures/Escherichia_coli/tRNA-Gly-CCC.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Gly-CCC.svg index c88c0233..12b4ef9a 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Gly-CCC.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Gly-CCC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="152.713" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Gly-CCC + @@ -30,19 +33,19 @@ d="M 76.6454 94.4085 L 80.5334 94.4085 "/> + d="M 55.0824 110.885 L 55.0824 114.773 "/> + d="M 47.5224 110.885 L 47.5224 114.773 "/> + d="M 39.9624 110.885 L 39.9624 114.773 "/> + d="M 32.4024 110.885 L 32.4024 114.773 "/> + d="M 69.7584 129.42 L 73.6464 129.42 "/> @@ -57,251 +60,245 @@ d="M 69.7584 159.66 L 73.6464 159.66 "/> + d="M 90.0703 107.803 L 90.0703 103.915 "/> + d="M 97.6303 107.803 L 97.6303 103.915 "/> + d="M 105.19 107.803 L 105.19 103.915 "/> + d="M 112.75 107.803 L 112.75 103.915 "/> - - - G - - - C 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-} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-CAG.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-CAG.svg index e122e81b..619648ae 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-CAG.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-CAG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.311" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Leu-CAG + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,302 +60,296 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 91.7766 117.916 L 94.5258 115.166 "/> + d="M 97.1223 123.261 L 99.8715 120.512 "/> + d="M 102.468 128.607 L 105.217 125.858 "/> + d="M 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+ G - - G + + G - - G + + G - - U + + G - - U + + U - - C + + U - - A + + C - - A + + A - - G + + A - - U + + G - - C + + U - - C + + C - - C + + C - - C + + C - - C + + C - - C + + C - - C + + C - - C + + C - - U + + C - - C + + U - - G + + C - - C + + G - - A + + C - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 45.4847 A 1.78191,1.78191 270 0,0 75.7018,43.7028L 72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-GAG.json b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-GAG.json index 6ca671f2..08a82afc 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-GAG.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-GAG.json @@ -3,530 +3,530 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 74.78, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 74.78, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 74.57, - "y": 81.98, + "y": 74.42, "pos": 4 }, { 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"<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.<<<<....>>>>..<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-GAG.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-GAG.svg index 549909da..1a79d77d 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-GAG.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-GAG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.311" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Leu-GAG + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,302 +60,296 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 91.7766 117.916 L 94.5258 115.166 "/> + d="M 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- G + + G - - G + + G - - C + + G - - U + + C - - U + + U - - A + + U - - C + + A - - G + + C - - G + + G - - G + + G - - U + + G - - U + + U - - C + + U - - A + + C - - A + + A - - G + + A - - U + + G - - C + + U - - C + + C - - C + + C - - G + + C - - U + + G - - C + + U - - C + + C - - U + + C - - C + + U - - G + + C - - G + + G - - U + + G - - A + + U - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 45.4847 A 1.78191,1.78191 270 0,0 75.7018,43.7028L 72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAA.json b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAA.json index 6cd7fac0..fcb0366b 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAA.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAA.json @@ -3,530 +3,530 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 74.78, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 74.78, - "y": 74.42, + "y": 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+ "y": 102.43, "pos": 75 }, { "base": "C", "x": 92.38, - "y": 109.99, + "y": 102.43, "pos": 76 }, { "base": "U", "x": 87.02, - "y": 104.66, + "y": 97.1, "pos": 77 }, { "base": "C", "x": 87.02, - "y": 97.1, + "y": 89.54, "pos": 78 }, { "base": "C", "x": 87.02, - "y": 89.54, + "y": 81.98, "pos": 79 }, { "base": "G", "x": 86.81, - "y": 81.98, + "y": 74.42, "pos": 80 }, { "base": "G", "x": 86.81, - "y": 74.42, + "y": 66.86, "pos": 81 }, { "base": "G", "x": 86.81, - "y": 66.86, + "y": 59.3, "pos": 82 }, { "base": "U", "x": 87.02, - "y": 59.3, + "y": 51.74, "pos": 83 }, { "base": "A", "x": 87.22, - "y": 51.74, + "y": 44.18, "pos": 84 }, { "base": "C", "x": 87.02, - "y": 44.18, + "y": 36.62, "pos": 85 }, { "base": "C", "x": 87.02, - "y": 36.62, + "y": 29.06, "pos": 86 }, { "base": "A", "x": 87.22, - "y": 29.06, + "y": 21.5, "pos": 87 } ], "width": 157.31, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Leu-TAA", "sequence": "GCCCGGAUGGUGGAAUCGGUAGACACAAGGGAUUUAAAAUCCCUCGGCGUUCGCGCUGUGCGGGUUCAAGUCCCGCUCCGGGUACCA", "structure": "<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>..<<<....>>>...<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAA.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAA.svg index 91e7f180..a9038828 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAA.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.311" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Leu-TAA + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,299 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"<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.<<<....>>>..<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAG.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAG.svg index 2a7df32f..25af5967 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAG.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Leu-TAG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.311" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Leu-TAG + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,293 +60,287 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 91.7766 117.916 L 94.5258 115.166 "/> + d="M 97.1223 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+ + G - - G + + C - - A + + G - - G + + A - - U + + G - - U + + U - - C + + U - - A + + C - - A + + A - - G + + A - - U + + G - - C + + U - - U + + C - - C + + U - - G + + C - - C + + G - - C + + C - - U + + C - - C + + U - - C + + C - - C + + C - - G + + C - - C + + G - - A + + C - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 45.4847 A 1.78191,1.78191 270 0,0 75.7018,43.7028L 72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Lys-TTT.json b/inst/extdata/structures/Escherichia_coli/tRNA-Lys-TTT.json index 9e4a420c..9b3e05e1 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Lys-TTT.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Lys-TTT.json @@ -3,464 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 71.51, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "G", "x": 71.51, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 71.72, - "y": 81.98, + "y": 74.42, 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21.5, "pos": 76 } ], "width": 154.67, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Lys-TTT", "sequence": "GGGUCGUUAGCUCAGUUGGUAGAGCAGUUGACUUUUAAUCAAUUGGUCGCAGGUUCGAAUCCUGCACGACCCACCA", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Lys-TTT.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Lys-TTT.svg index fa8580d9..42f03df7 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Lys-TTT.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Lys-TTT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Lys-TTT + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 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87.22, - "y": 29.06, + "y": 21.5, "pos": 77 } ], "width": 157.73, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Met-CAT", "sequence": "GGCUACGUAGCUCAGUUGGUUAGAGCACAUCACUCAUAAUGAUGGGGUCACAGGUUCGAAUCCCGUCGUAGCCACCA", "structure": "<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Met-CAT.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Met-CAT.svg index 04b8bb97..95561b42 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Met-CAT.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Met-CAT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Met-CAT + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 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b/inst/extdata/structures/Escherichia_coli/tRNA-Ser-GCT.json index 795ce83d..83441ffe 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Ser-GCT.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Ser-GCT.json @@ -3,566 +3,566 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 74.57, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "U", "x": 74.78, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 74.57, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "A", "x": 74.98, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "G", "x": 74.57, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "G", "x": 74.57, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 67.34, - "y": 106.05, + "y": 98.49, "pos": 8 }, { "base": "G", "x": 60.96, - "y": 110.42, + "y": 102.86, "pos": 9 }, { "base": "G", "x": 57.18, - "y": 116.96, + "y": 109.4, "pos": 10 }, { "base": "C", "x": 49.83, - "y": 116.96, + "y": 109.4, "pos": 11 }, { "base": "C", 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"<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.<<<<<<<.....>>>>>>>.<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Ser-GCT.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Ser-GCT.svg index 9719971c..2ebbf6f5 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Ser-GCT.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Ser-GCT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Ser-GCT + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,329 +60,323 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 91.7766 117.916 L 94.5258 115.166 "/> + d="M 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C - - G + + C - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 45.4847 A 1.78191,1.78191 270 0,0 75.7018,43.7028L 72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Thr-CGT.json b/inst/extdata/structures/Escherichia_coli/tRNA-Thr-CGT.json index f4d6a913..f856f69a 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Thr-CGT.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Thr-CGT.json @@ -3,464 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 71.51, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "A", "x": 71.92, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "U", "x": 71.72, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "A", "x": 71.92, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 64.29, - "y": 106.05, + "y": 98.49, 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"<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Thr-CGT.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Thr-CGT.svg index 0486d243..50de43f4 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Thr-CGT.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Thr-CGT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Thr-CGT + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 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"<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Thr-GGT.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Thr-GGT.svg index 99f9986e..d282d292 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Thr-GGT.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Thr-GGT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Thr-GGT + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 L 99.5865 103.915 "/> + d="M 107.146 107.803 L 107.146 103.915 "/> + d="M 114.706 107.803 L 114.706 103.915 "/> - - - G - - - C + d="M 122.266 107.803 L 122.266 103.915 "/> + + G - - U + + C - - G + + U - - A + + G - - U + + A - - A + + U - - U + + A - - A + + U - - G + + A - - C + + G - - U + + C - - C + + U - - A + + C - - G + + A - - U + + G - - U + + U - - G + + U - - G + + G - - U + + G - - A + + U - - G + + A - - A + + G - - G + + A - - C + + G - - G + + C - - C + + G - - A + + C - - C + + A - - C + + C - - C + + C - - U + + C - - U + + U - - G + + U - - G + + G - - U + + G - - A + + U - - A + + A - - G + + A - - G + + G - - G + + G - - U + + G - - G + + U - - A + + G - - G + + A - - G + + G - - U + + G - - C + + U - - G + + C - - G + + G - - C + + G - - A + + C - - G + + A - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - A + + A - - U + + A - - C + + U - - U + + C - - G + + U - - C + + G - - C + + C - - U + + C - - A + + U - - U + + A - - C + + U - - A + + C - - G + + A - - C + + G - - A + + C - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Thr-TGT.json b/inst/extdata/structures/Escherichia_coli/tRNA-Thr-TGT.json index 74dd1213..ef1ce8a1 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Thr-TGT.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Thr-TGT.json @@ -3,464 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 71.51, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "A", "x": 71.92, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "C", "x": 71.72, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "U", "x": 71.72, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 64.29, - "y": 106.05, 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"<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Thr-TGT.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Thr-TGT.svg index b094d381..ac503632 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Thr-TGT.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Thr-TGT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Thr-TGT + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 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"<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Trp-CCA.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Trp-CCA.svg index 2e4a603c..3ea9d49d 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Trp-CCA.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Trp-CCA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Trp-CCA + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 L 99.5865 103.915 "/> + d="M 107.146 107.803 L 107.146 103.915 "/> + d="M 114.706 107.803 L 114.706 103.915 "/> - - - A - - - G + d="M 122.266 107.803 L 122.266 103.915 "/> + + A - - G + + G - - G + + G - - G + + G - - C + + G - - G + + C - - U + + G - - A + + U - - G + + A - - U + + G - - U + + U - - C + + U - - A + + C - - A + + A - - U + + A - - U + + U - - G + + U - - G + + G - - U + + G - - A + + U - - G + + A - - A + + G - - G + + A - - C + + G - - A + + C - - C + + A - - C + + C - - G + + C - - G + + G - - U + + G - - C + + U - - U + + C - - C + + U - - C + + C - - A + + C - - A + + A - - A + + A - - A + + A - - C + + A - - C + + C - - G + + C - - G + + G - - G + + G - - U + + G - - G + + U - - U + + G - - U + + U - - G + + U - - G + + G - - G + + G - - A + + G - - G + + A - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - G + + A - - U + + G - - C + + U - - U + + C - - C + + U - - U + + C - - C + + U - - C + + C - - G + + C - - C + + G - - C + + C - - C + + C - - C + + C - - U + + C - - G + + U - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Tyr-GTA.json b/inst/extdata/structures/Escherichia_coli/tRNA-Tyr-GTA.json index 237e0e54..1655c6cb 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Tyr-GTA.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Tyr-GTA.json @@ -3,518 +3,518 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 74.57, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "U", "x": 74.78, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 74.57, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "G", "x": 74.57, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "G", "x": 74.57, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "G", "x": 74.57, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 67.34, - "y": 106.05, 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b/inst/extdata/structures/Escherichia_coli/tRNA-Tyr-GTA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Tyr-GTA + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,293 +60,287 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 91.7766 117.916 L 94.5258 115.166 "/> + d="M 97.1223 123.261 L 99.8715 120.512 "/> + d="M 102.468 128.607 L 105.217 125.858 "/> + d="M 95.0847 107.803 L 95.0847 103.915 "/> + d="M 102.645 107.803 L 102.645 103.915 "/> + d="M 110.205 107.803 L 110.205 103.915 "/> + d="M 117.765 107.803 L 117.765 103.915 "/> - - - G - - - G + d="M 125.325 107.803 L 125.325 103.915 "/> + + G - - U + + G - - G + + U - - G + + G - - G + + G - - G + + G - - U + + G - - U + + U - - C + + U - - C + + C - - C + + C - - G + + C - - A + + G - - G + + A - - C + + G - - G + + C - - G + + G - - C + + G - - C + + C - - A + + C - - A + + A - - A + + A - - G + + A - - G + + G - - G + + G - - A + + G - - G + + A - - C + + G - - A + + C - - G + + A - - A + + G - - C + + A - - U + + C - - G + + U - - U + + G - - A + + U - - A + + A - - A + + A - - U + + A - - C + + U - - U + + C - - G + + U - - C + + G - - C + + C - - G + + C - - U + + G - - C + + U - - A + + C - - C + + A - - A + + C - - G + + A - - A + + G - - C + + A - - U + + C - - U + + U - - C + + U - - G + + C - - A + + G - - A + + A - - G + + A - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - A + + A - - U + + A - - C + + U - - C + + C - - U + + C - - U + + U - - C + + U - - C + + C - - C + + C - - C + + C - - C + + C - - A + + C - - C + + A - - C + + C - - A + + C - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 45.4847 A 1.78191,1.78191 270 0,0 75.7018,43.7028L 72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Val-GAC.json b/inst/extdata/structures/Escherichia_coli/tRNA-Val-GAC.json index 3ff33550..aeeaa145 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Val-GAC.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Val-GAC.json @@ -3,470 +3,470 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 74.78, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "G", "x": 74.57, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 74.78, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 74.78, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "C", "x": 74.78, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "G", "x": 74.57, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 67.34, - "y": 106.05, + "y": 98.49, "pos": 8 }, { "base": "A", "x": 61.38, - "y": 110.42, + "y": 102.86, "pos": 9 }, { 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"<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Val-GAC.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Val-GAC.svg index 5ff9cb5c..0d8cc25a 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Val-GAC.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Val-GAC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Val-GAC + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,260 +60,254 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 95.0847 107.803 L 95.0847 103.915 "/> + d="M 102.645 107.803 L 102.645 103.915 "/> + d="M 110.205 107.803 L 110.205 103.915 "/> + d="M 117.765 107.803 L 117.765 103.915 "/> - - - G - - - C + d="M 125.325 107.803 L 125.325 103.915 "/> + + G - - G + + C - - U + + G - - C + + U - - C + + C - - G + + C - - U + + G - - A + + U - - G + + A - - C + + G - - U + + C - - C + + U - - A + + C - - G + + A - - U + + G - - U + + U - - G + + U - - G + + G - - U + + G - - U + + U - - A + + U - - G + + A - - A + + G - - G + + A - - C + + G - - A + + C - - C + + A - - C + + C - - A + + C - - C + + A - - C + + C - - U + + C - - U + + U - - G + + U - - A + + G - - C + + A - - A + + C - - U + + A - - G + + U - - G + + G - - U + + G - - G + + U - - G + + G - - G + + G - - G + + G - - G + + G - - U + + G - - C + + U - - G + + C - - G + + G - - U + + G - - G + + U - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - G + + A - - U + + G - - C + + U - - C + + C - - A + + C - - C + + A - - U + + C - - C + + U - - G + + C - - G + + G - - A + + G - - C + + A - - G + + C - - C + + G - - A + + C - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 45.4847 A 1.78191,1.78191 270 0,0 75.7018,43.7028L 72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Val-TAC.json b/inst/extdata/structures/Escherichia_coli/tRNA-Val-TAC.json index 254f0371..2883a90e 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Val-TAC.json +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Val-TAC.json @@ -3,464 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 71.51, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "G", "x": 71.51, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 71.72, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "G", "x": 71.51, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "A", "x": 71.92, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "U", "x": 71.72, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 64.29, - 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22 }, { "base": "A", "x": 39.42, - "y": 129.2, + "y": 121.64, "pos": 23 }, { "base": "G", "x": 46.56, - "y": 129.2, + "y": 121.64, "pos": 24 }, { "base": "C", "x": 54.33, - "y": 129.2, + "y": 121.64, "pos": 25 }, { "base": "A", "x": 58.74, - "y": 135.48, + "y": 127.92, "pos": 26 }, { "base": "C", "x": 64.83, - "y": 139.67, + "y": 132.11, "pos": 27 }, { "base": "C", "x": 64.83, - "y": 147.23, + "y": 139.67, "pos": 28 }, { "base": "U", "x": 64.83, - "y": 154.79, + "y": 147.23, "pos": 29 }, { "base": "C", "x": 64.83, - "y": 162.35, + "y": 154.79, "pos": 30 }, { "base": "C", "x": 64.83, - "y": 169.91, + "y": 162.35, "pos": 31 }, { "base": "C", "x": 59.94, - "y": 175.68, + "y": 168.12, "pos": 32 }, { "base": "U", "x": 59.54, - "y": 183.23, + "y": 175.67, "pos": 33 }, { "base": "U", "x": 63.79, - "y": 189.49, + "y": 181.93, "pos": 34 }, { "base": "A", "x": 71.16, - "y": 191.9, + "y": 184.34, "pos": 35 }, { "base": "C", "x": 78.12, - "y": 189.49, + "y": 181.93, "pos": 36 }, { "base": "A", 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"<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/tRNA-Val-TAC.svg b/inst/extdata/structures/Escherichia_coli/tRNA-Val-TAC.svg index e42c131d..7680a8ae 100644 --- a/inst/extdata/structures/Escherichia_coli/tRNA-Val-TAC.svg +++ b/inst/extdata/structures/Escherichia_coli/tRNA-Val-TAC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Val-TAC + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 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b/inst/extdata/structures/Escherichia_coli/tRNA-fMet-CAT.svg @@ -0,0 +1,313 @@ + + + tRNA-fMet-CAT + + + + + + + + + + + + + + + + + + + + + + + + C + + + G + + + C + + + G + + + G + + + G + + + G + + + U + + + G + + + G + + + A + + + G + + + C + + + A + + + G + + + C + + + C + + + U + + + G + + + G + + + U + + + A + + + G + + + C + + + U + + + C + + + G + + + U + + + C + + + G + + + G + + + G + + + C + + + U + + + C + + + A + + + U + + + A + + + A + + + C + + + C + + + C + + + G + + + A + + + A + + + G + + + G + + + U + + + C + + + G + + + U + + + C + + + G + + + G + + + U + + + U + + + C + + + A + + + A + + + A + + + U + + + C + + + C + + + G + + + G + + + C + + + C + + + C + + + C + + + C + + + G + + + C + + + A + + + A + + + C + + + C + + + A + + + + 5' + + diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Ala-AGC.json b/inst/extdata/structures/Homo_sapiens/tRNA-Ala-AGC.json index f7315891..fb069fd6 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Ala-AGC.json +++ 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"y": 21.5, "pos": 72 } ], "width": 152.71, - "height": 176.72, + "height": 169.16, "lines": [], "trna_name": "tRNA-Ala-AGC", "sequence": "GGGGGUAUAGCUCAGUGGUAGAGCGCGUGCUUAGCAUGCACGAGGUCCUGGGUUCGAUCCCCAGUACCUCCA", "structure": "<<<<<<<..<<<<.......>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Ala-AGC.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Ala-AGC.svg index 7dac0624..6a8cf00d 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Ala-AGC.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Ala-AGC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="152.713" - height="176.717" + height="169.157" id="svg2403" xml:space="preserve"> tRNA-Ala-AGC + @@ -30,19 +33,19 @@ d="M 76.6454 71.7285 L 80.5334 71.7285 "/> + d="M 55.0824 88.2051 L 55.0824 92.0931 "/> + d="M 47.5224 88.2051 L 47.5224 92.0931 "/> + d="M 39.9624 88.2051 L 39.9624 92.0931 "/> + d="M 32.4024 88.2051 L 32.4024 92.0931 "/> + d="M 69.7584 106.74 L 73.6464 106.74 "/> @@ -57,245 +60,239 @@ d="M 69.7584 136.98 L 73.6464 136.98 "/> + d="M 90.0703 85.123 L 90.0703 81.235 "/> + d="M 97.6303 85.123 L 97.6303 81.235 "/> + d="M 105.19 85.123 L 105.19 81.235 "/> + d="M 112.75 85.123 L 112.75 81.235 "/> - - - G - - - G + d="M 120.31 85.123 L 120.31 81.235 "/> + + G - - G + + G - - G + + G - - G + + G - - U + + G - - A + + U - - U + + A - - A + + U - - G + + A - - C + + G - - U + + C - - C + + U - - A + + C - - G + + A - - U + + G - - G + + U - - G + + G - - U + + G - - A + + U - - G + + A - - A + + G - - G + + A - - C + + G - - G + + C - - C + + G - - G + + C - - U + + G - - G + + U - - C + + G - - U + + C - - U + + U - - A + + U - - G + + A - - C + + G - - A + + C - - U + + A - - G + + U - - C + + G - - A + + C - - C + + A - - G + + C - - A + + G - - G + + A - - G + + G - - U + + G - - C + + U - - C + + C - - U + + C - - G + + U - - G + + G - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - U + + A - - C + + U - - C + + C - - C + + C - - C + + C - - A + + C - - G + + A - - U + + G - - A + + U - - C + + A - - C + + C - - U + + C - - C + + U - - C + + C - - A + + C - - A + + A - - 5' + d="M 72.4694 22.8047 A 1.78191,1.78191 270 0,0 70.6875,21.0228L 67.1236 21.0228 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Ala-CGC.json b/inst/extdata/structures/Homo_sapiens/tRNA-Ala-CGC.json index 4af004cb..4c6eec40 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Ala-CGC.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Ala-CGC.json @@ -3,440 +3,440 @@ { "base": "G", "x": 69.55, - "y": 36.62, + "y": 29.06, "pos": 1 }, { "base": "G", "x": 69.55, - "y": 44.18, + "y": 36.62, "pos": 2 }, { "base": "G", "x": 69.55, - "y": 51.74, + "y": 44.18, "pos": 3 }, { "base": "G", "x": 69.55, - "y": 59.3, + "y": 51.74, "pos": 4 }, { "base": "A", "x": 69.97, - "y": 66.86, + "y": 59.3, "pos": 5 }, { "base": "U", "x": 69.76, - "y": 74.42, + 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"base": "G", "x": 102.27, - "y": 99.55, + "y": 91.99, "pos": 50 }, { "base": "G", "x": 109.83, - "y": 99.55, + "y": 91.99, "pos": 51 }, { "base": "G", "x": 117.39, - "y": 99.55, + "y": 91.99, "pos": 52 }, { "base": "U", "x": 123.37, - "y": 104.44, + "y": 96.88, "pos": 53 }, { "base": "U", "x": 130.92, - "y": 104.84, + "y": 97.28, "pos": 54 }, { "base": "C", "x": 137.18, - "y": 100.6, + "y": 93.04, "pos": 55 }, { "base": "G", "x": 139.38, - "y": 93.43, + "y": 85.87, "pos": 56 }, { "base": "A", "x": 137.38, - "y": 86.27, + "y": 78.71, "pos": 57 }, { "base": "U", "x": 130.92, - "y": 82.02, + "y": 74.46, "pos": 58 }, { "base": "C", "x": 123.37, - "y": 82.42, + "y": 74.86, "pos": 59 }, { "base": "C", "x": 117.6, - "y": 87.31, + "y": 79.75, "pos": 60 }, { "base": "C", "x": 110.04, - "y": 87.31, + "y": 79.75, "pos": 61 }, { "base": "C", "x": 102.48, - "y": 87.31, + "y": 79.75, "pos": 62 }, { "base": "G", "x": 94.71, - "y": 87.31, + "y": 79.75, "pos": 63 }, { "base": "G", "x": 87.15, - "y": 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b/inst/extdata/structures/Homo_sapiens/tRNA-Ala-CGC.svg index 5cb58e0c..e502e478 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Ala-CGC.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Ala-CGC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="152.713" - height="176.717" + height="169.157" id="svg2403" xml:space="preserve"> tRNA-Ala-CGC + @@ -30,19 +33,19 @@ d="M 76.6454 71.7285 L 80.5334 71.7285 "/> + d="M 55.0824 88.2051 L 55.0824 92.0931 "/> + d="M 47.5224 88.2051 L 47.5224 92.0931 "/> + d="M 39.9624 88.2051 L 39.9624 92.0931 "/> + d="M 32.4024 88.2051 L 32.4024 92.0931 "/> + d="M 69.7584 106.74 L 73.6464 106.74 "/> @@ -57,245 +60,239 @@ d="M 69.7584 136.98 L 73.6464 136.98 "/> + d="M 90.0703 85.123 L 90.0703 81.235 "/> + d="M 97.6303 85.123 L 97.6303 81.235 "/> + d="M 105.19 85.123 L 105.19 81.235 "/> + d="M 112.75 85.123 L 112.75 81.235 "/> - - - G - - - G + d="M 120.31 85.123 L 120.31 81.235 "/> + + G - - G + + G - - G + + G - - A + + G - - U + + A - - G + + U - - U + + G - - A + + U - - G + + A - - C + + G - - U + + C - - C + + U - - A + + C - - G + + A - - U + + G - - G + + U - - G + + G - - U + + G - - A + + U - - G + + A - - A + + G - - G + + A - - C + + G - - G + + C - - C + + G - - A + + C - - U + + A - - G + + U - - C + + G - - U + + C - - U + + U - - C + + U - - G + + C - - C + + G - - A + + C - - U + + A - - G + + U - - U + + G - - A + + U - - U + + A - - G + + U - - A + + G - - G + + A - - G + + G - - U + + G - - C + + U - - C + + C - - C + + C - - G + + C - - G + + G - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - U + + A - - C + + U - - C + + C - - C + + C - - C + + C - - G + + C - - G + + G - - C + + G - - A + + C - - U + + A - - C + + U - - U + + C - - C + + U - - C + + C - - A + + C - - A + + A - - 5' + d="M 72.4694 22.8047 A 1.78191,1.78191 270 0,0 70.6875,21.0228L 67.1236 21.0228 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Ala-TGC.json 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+ d="M 55.0824 88.2051 L 55.0824 92.0931 "/> + d="M 47.5224 88.2051 L 47.5224 92.0931 "/> + d="M 39.9624 88.2051 L 39.9624 92.0931 "/> + d="M 32.4024 88.2051 L 32.4024 92.0931 "/> + d="M 69.7584 106.74 L 73.6464 106.74 "/> @@ -57,245 +60,239 @@ d="M 69.7584 136.98 L 73.6464 136.98 "/> + d="M 90.0703 85.123 L 90.0703 81.235 "/> + d="M 97.6303 85.123 L 97.6303 81.235 "/> + d="M 105.19 85.123 L 105.19 81.235 "/> + d="M 112.75 85.123 L 112.75 81.235 "/> - - - G - - - G + d="M 120.31 85.123 L 120.31 81.235 "/> + + G - - G + + G - - G + + G - - G + + G - - U + + G - - G + + U - - U + + G - - A + + U - - G + + A - - C + + G - - U + + C - - C + + U - - A + + C - - G + + A - - U + + G - - G + + U - - G + + G - - U + + G - - A + + U - - G + + A - - A + + G - - G + + A - - C + + G - - G + + C - - C + + G - - A + + C - - U + + A - - G + + U - - C + + G - - U + + C - - U + + U - - U + + U - - G + + U - - C + + G - - A + + C - - U + + A - - G + + U - - U + + G - - A + + U - - U + + A - - G + + U - - A + + G - - G + + A - - G + + G - - U + + G - - C + + U - - C + + C - - C + + C - - G + + C - - G + + G - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - U + + A - - C + + U - - C + + C - - C + + C - - C + + C - - G + + C - - G + + G - - C + + G - - A + + C - - C + + A - - C + + C - - U + + C - - C + + U - - C + + C - - A + + C - - A + + A - - 5' + d="M 72.4694 22.8047 A 1.78191,1.78191 270 0,0 70.6875,21.0228L 67.1236 21.0228 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Arg-ACG.json b/inst/extdata/structures/Homo_sapiens/tRNA-Arg-ACG.json index c391fe78..ec4d345e 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Arg-ACG.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Arg-ACG.json @@ -3,446 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 71.51, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "G", "x": 71.51, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "C", "x": 71.72, - "y": 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"y": 21.5, + "pos": 76 } ], "width": 154.67, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Arg-ACG", "sequence": "GGGCCAGUGGCGCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCUGGCUCG", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Arg-ACG.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Arg-ACG.svg index 17a870d8..6314f590 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Arg-ACG.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Arg-ACG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Arg-ACG + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 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"structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCG.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCG.svg index a77fec09..3f4e142d 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCG.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Arg-TCG + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 L 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+ G - - C + + U - - G + + C - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCT.json b/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCT.json index ef59012d..9ef48c60 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCT.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCT.json @@ -3,446 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 71.51, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 71.72, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 71.72, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "C", "x": 71.72, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "G", "x": 71.51, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 64.29, - "y": 106.05, + "y": 98.49, 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"<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCT.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCT.svg index 4fdc81eb..b056932d 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCT.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Arg-TCT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Arg-TCT + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 L 99.5865 103.915 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- - G + + C - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Asn-GTT.json b/inst/extdata/structures/Homo_sapiens/tRNA-Asn-GTT.json index b253a9b9..9d1b1ccf 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Asn-GTT.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Asn-GTT.json @@ -3,452 +3,470 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "U", "x": 74.78, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 74.78, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 74.78, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 74.78, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "U", "x": 74.78, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "G", "x": 74.57, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 67.34, - "y": 106.05, + "y": 98.49, "pos": 8 }, { "base": "G", "x": 60.96, - "y": 110.42, + "y": 102.86, "pos": 9 }, { "base": "G", "x": 57.18, - "y": 116.96, + "y": 109.4, "pos": 10 }, { "base": "C", "x": 49.83, - "y": 116.96, + "y": 109.4, "pos": 11 }, { "base": "G", "x": 42.06, - "y": 116.96, + "y": 109.4, "pos": 12 }, { "base": "C", "x": 34.71, - "y": 116.96, + "y": 109.4, "pos": 13 }, { "base": "A", "x": 29.96, - "y": 111.25, + "y": 103.69, "pos": 14 }, { "base": "A", "x": 22.77, - "y": 108.9, + "y": 101.34, "pos": 15 }, { "base": "U", "x": 15.19, - "y": 110.58, + "y": 103.02, "pos": 16 }, { "base": "C", "x": 9.72, - "y": 115.8, + "y": 108.23, "pos": 17 }, { "base": "G", "x": 7.5, - "y": 123.08, + "y": 115.52, "pos": 18 }, { "base": "G", "x": 9.51, - "y": 130.37, + "y": 122.81, "pos": 19 }, { "base": "U", "x": 15.19, - "y": 135.59, + "y": 128.03, "pos": 20 }, { "base": "U", "x": 22.57, - "y": 137.26, + "y": 129.7, "pos": 21 }, { "base": "A", "x": 29.96, - "y": 134.91, + "y": 127.35, "pos": 22 }, { "base": "G", "x": 34.5, - "y": 129.2, + "y": 121.64, "pos": 23 }, { "base": "C", "x": 42.27, - "y": 129.2, + "y": 121.64, "pos": 24 }, { "base": "G", "x": 49.62, - "y": 129.2, + "y": 121.64, "pos": 25 }, { "base": "C", "x": 57.39, - "y": 129.2, + "y": 121.64, "pos": 26 }, { "base": "G", "x": 61.39, - "y": 135.48, + "y": 127.92, "pos": 27 }, { "base": "U", "x": 67.89, - "y": 139.67, + "y": 132.11, "pos": 28 }, { "base": "U", "x": 67.89, - "y": 147.23, + "y": 139.67, "pos": 29 }, { "base": "C", "x": 67.89, - "y": 154.79, + "y": 147.23, "pos": 30 }, { "base": "G", "x": 67.68, - "y": 162.35, + "y": 154.79, "pos": 31 }, { "base": "G", "x": 67.68, - "y": 169.91, + "y": 162.35, "pos": 32 }, { "base": "C", "x": 63.0, - "y": 175.68, + "y": 168.12, "pos": 33 }, { "base": "U", "x": 62.6, - "y": 183.23, + "y": 175.67, "pos": 34 }, { "base": "G", "x": 66.63, - "y": 189.49, + "y": 181.93, "pos": 35 }, { "base": "U", "x": 74.01, - "y": 191.9, + "y": 184.34, "pos": 36 }, { "base": "U", "x": 81.17, - "y": 189.49, + "y": 181.93, 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"base": "U", "x": 107.5, - "y": 122.23, + "y": 114.67, "pos": 52 }, { "base": "G", "x": 114.85, - "y": 122.23, + "y": 114.67, "pos": 53 }, { "base": "G", "x": 122.41, - "y": 122.23, + "y": 114.67, "pos": 54 }, { "base": "U", "x": 128.38, - "y": 127.12, + "y": 119.56, "pos": 55 }, { "base": "U", "x": 135.93, - "y": 127.52, + "y": 119.96, "pos": 56 }, { "base": "C", "x": 142.19, - "y": 123.28, + "y": 115.72, "pos": 57 }, { "base": "G", "x": 144.39, - "y": 116.11, + "y": 108.55, "pos": 58 }, { "base": "A", "x": 142.4, - "y": 108.95, + "y": 101.39, "pos": 59 }, { "base": "U", "x": 135.93, - "y": 104.7, + "y": 97.14, "pos": 60 }, { "base": "C", "x": 128.38, - "y": 105.1, + "y": 97.54, "pos": 61 }, { "base": "C", "x": 122.62, - "y": 109.99, + "y": 102.43, "pos": 62 }, { "base": "C", "x": 115.06, - "y": 109.99, + "y": 102.43, "pos": 63 }, { "base": "A", "x": 107.7, - "y": 109.99, + "y": 102.43, "pos": 64 }, { "base": "C", "x": 99.94, - "y": 109.99, + "y": 102.43, "pos": 65 }, { "base": "C", "x": 92.38, - "y": 109.99, + "y": 102.43, "pos": 66 }, { "base": "C", "x": 87.02, - "y": 104.66, + "y": 97.1, "pos": 67 }, { "base": "A", "x": 87.22, - "y": 97.1, + "y": 89.54, "pos": 68 }, { "base": "G", "x": 86.81, - "y": 89.54, + "y": 81.98, "pos": 69 }, { "base": "G", "x": 86.81, - "y": 81.98, + "y": 74.42, "pos": 70 }, { "base": "G", "x": 86.81, - "y": 74.42, + "y": 66.86, "pos": 71 }, { "base": "A", "x": 87.22, - "y": 66.86, + "y": 59.3, "pos": 72 }, { "base": "C", "x": 87.02, - "y": 59.3, + "y": 51.74, "pos": 73 }, { "base": "G", "x": 86.81, - "y": 51.74, + "y": 44.18, "pos": 74 + }, + { + "base": "C", + "x": 87.02, + "y": 36.62, + "pos": 75 + }, + { + "base": "C", + "x": 87.02, + "y": 29.06, + "pos": 76 + }, + { + "base": "A", + "x": 87.22, + "y": 21.5, + "pos": 77 } ], "width": 157.73, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Asn-GTT", "sequence": "GUCUCUGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAUCCCACCCAGGGACG", "structure": "<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Asn-GTT.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Asn-GTT.svg index fc612eb1..df09936f 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Asn-GTT.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Asn-GTT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Asn-GTT + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,260 +60,254 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 95.0847 107.803 L 95.0847 103.915 "/> + d="M 102.645 107.803 L 102.645 103.915 "/> + d="M 110.205 107.803 L 110.205 103.915 "/> + d="M 117.765 107.803 L 117.765 103.915 "/> - - - G - - - U + d="M 125.325 107.803 L 125.325 103.915 "/> + + G - - C + + U - - U + + C - - C + + U - - U + + C - - G + + U - - U + + G - - G + + U - - G + + G - - C + + G - - G + + C - - C + + G - - A + + C - - A + + A - - U + + A - - C + + U - - G + + C - - G + + G - - U + + G - - U + + U - - A + + U - - G + + A - - C + + G - - G + + C - - C + + G - - G + + C - - U + + G - - U + + U - - C + + U - - G + + C - - G + + G - - C + + G - - U + + C - - G + + U - - U + + G - - U + + U - - A + + U - - A + + A - - C + + A - - C + + C - - G + + C - - A + + G - - A + + A - - A + + A - - G + + A - - G + + G - - U + + G - - U + + U - - G + + U - - G + + G - - U + + G - - G + + U - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - U + + A - - C + + U - - C + + C - - C + + C - - A + + C - - C + + A - - C + + C - - C + + C - - A + + C - - G + + A - - G + + G - - G + + G - - A + + G - - C + + A - - G + + C - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 45.4847 A 1.78191,1.78191 270 0,0 75.7018,43.7028L 72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Asp-GTC.json b/inst/extdata/structures/Homo_sapiens/tRNA-Asp-GTC.json index 7e92674a..e7e0751f 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Asp-GTC.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Asp-GTC.json @@ -3,440 +3,458 @@ { "base": "U", "x": 71.72, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 71.72, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 71.72, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "G", "x": 71.51, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "U", "x": 71.72, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 64.29, - "y": 106.05, + "y": 98.49, "pos": 8 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a/inst/extdata/structures/Homo_sapiens/tRNA-Asp-GTC.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Asp-GTC.svg index 01525b68..fb151f55 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Asp-GTC.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Asp-GTC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.253" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Asp-GTC + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,254 +60,248 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 L 99.5865 103.915 "/> + d="M 107.146 107.803 L 107.146 103.915 "/> + d="M 114.706 107.803 L 114.706 103.915 "/> - - - U - - - C + d="M 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72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Cys-GCA.json b/inst/extdata/structures/Homo_sapiens/tRNA-Cys-GCA.json index a3b0cde0..ab716f0d 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Cys-GCA.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Cys-GCA.json @@ -3,440 +3,458 @@ { "base": "G", "x": 69.55, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 69.55, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "G", "x": 69.55, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 69.55, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "G", "x": 69.55, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "C", "x": 69.76, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "A", "x": 69.97, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 62.33, - "y": 106.05, + "y": 98.49, "pos": 8 }, { "base": "A", "x": 56.37, - "y": 110.42, + "y": 102.86, "pos": 9 }, { "base": "G", "x": 52.16, - "y": 116.96, + "y": 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"pos": 75 } ], "width": 154.67, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Glu-CTC", "sequence": "UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Glu-CTC.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Glu-CTC.svg index 5f501a27..a3dcc58e 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Glu-CTC.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Glu-CTC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Glu-CTC + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,254 +60,248 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 L 99.5865 103.915 "/> + d="M 107.146 107.803 L 107.146 103.915 "/> + d="M 114.706 107.803 L 114.706 103.915 "/> - - - U - - - C + d="M 122.266 107.803 L 122.266 103.915 "/> + + U - - C + + C - - C + + C - - U + + C - - G + + U - - G + + G - - U + + G - - G + + U - - G + + G - - U + + G - - C + + U - - U + + C - - A + + U - - G + + A - - U + + G - - G + + U - - G + + G - - U + + G - - U + + U - - A + + U - - G + + A - - G + + G - - A + + G - - U + + A - - U + + U - - C + + U - - G + + C - - G + + G - - C + + G - - G + + C - - C + + G - - U + + C - - C + + U - - U + + C - - C + + U - - A + + C - - C + + A - - C + + C - - G + + C - - C + + G - - C + + C - - G + + C - - C + + G - - G + + C - - G + + G - - C + + G - - C + + C - - C + + C - - G + + C - - G + + G - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - U + + A - - U + + U - - C + + U - - C + + C - - C + + C - - G + + C - - G + + G - - U + + G - - C + + U - - A + + C - - G + + A - - G + + G - - G + + G - - A + + G - - A + + A - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Glu-TTC.json b/inst/extdata/structures/Homo_sapiens/tRNA-Glu-TTC.json index 9a7f3d21..9556feb6 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Glu-TTC.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Glu-TTC.json @@ -3,440 +3,458 @@ { "base": "U", "x": 71.72, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "C", "x": 71.72, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "A", "x": 71.92, - "y": 89.54, + "y": 81.98, "pos": 5 }, { 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"UCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAA", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Glu-TTC.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Glu-TTC.svg index b020e6e4..138ca1de 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Glu-TTC.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Glu-TTC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Glu-TTC + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,254 +60,248 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> 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G - - A + + U - - U + + A - - G + + U - - G + + G - - G + + G - - A + + G - - A + + A - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Gly-CCC.json b/inst/extdata/structures/Homo_sapiens/tRNA-Gly-CCC.json index 2bf4cd88..27c9691b 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Gly-CCC.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Gly-CCC.json @@ -3,434 +3,452 @@ { "base": "G", "x": 69.55, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 69.76, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "A", "x": 69.97, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 69.76, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "U", "x": 69.76, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "G", "x": 69.55, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "G", "x": 69.55, - "y": 104.66, + "y": 97.1, "pos": 7 }, { 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"x": 83.96, + "y": 29.06, + "pos": 74 + }, + { + "base": "A", + "x": 84.16, + "y": 21.5, + "pos": 75 } ], "width": 154.67, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-His-GTG", "sequence": "GCCGUGAUCGUAUAGUGGUUAGUACUCUGCGUUGUGGCCGCAGCAACCUCGGUUCGAAUCCGAGUCACGGCA", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-His-GTG.svg b/inst/extdata/structures/Homo_sapiens/tRNA-His-GTG.svg index c0a7b939..c5f0755d 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-His-GTG.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-His-GTG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-His-GTG + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 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A - - C + + C - - U + + C - - C + + U - - G + + C - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - A + + A - - U + + A - - C + + U - - C + + C - - G + + C - - A + + G - - G + + A - - U + + G - - C + + U - - A + + C - - C + + A - - G + + C - - G + + G - - C + + G - - A + + C - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Ile-AAT.json b/inst/extdata/structures/Homo_sapiens/tRNA-Ile-AAT.json index cc9b7632..2735d914 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Ile-AAT.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Ile-AAT.json @@ -3,452 +3,452 @@ { "base": "G", "x": 74.57, - "y": 36.62, + "y": 29.06, "pos": 1 }, { "base": "G", "x": 74.57, - "y": 44.18, + "y": 36.62, "pos": 2 }, { "base": "C", "x": 74.78, - "y": 51.74, + "y": 44.18, "pos": 3 }, { "base": "C", "x": 74.78, - "y": 59.3, + "y": 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"GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGCGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA", "structure": "<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Ile-AAT.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Ile-AAT.svg index 86b31df8..5e600897 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Ile-AAT.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Ile-AAT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="176.717" + height="169.157" id="svg2403" xml:space="preserve"> tRNA-Ile-AAT + @@ -30,19 +33,19 @@ d="M 81.6597 71.7285 L 85.5477 71.7285 "/> + d="M 60.0967 88.2051 L 60.0967 92.0931 "/> + d="M 52.5367 88.2051 L 52.5367 92.0931 "/> + d="M 44.9767 88.2051 L 44.9767 92.0931 "/> + d="M 37.4167 88.2051 L 37.4167 92.0931 "/> + d="M 74.7728 106.74 L 78.6608 106.74 "/> @@ -57,251 +60,245 @@ d="M 74.7728 136.98 L 78.6608 136.98 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U + + G - - A + + U - - C + + A - - G + + C - - G + + G - - G + + G - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 22.8047 A 1.78191,1.78191 270 0,0 75.7018,21.0228L 72.138 21.0228 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Ile-GAT.json b/inst/extdata/structures/Homo_sapiens/tRNA-Ile-GAT.json index 592f9e75..59cafdfe 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Ile-GAT.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Ile-GAT.json @@ -3,452 +3,452 @@ { "base": "G", "x": 74.57, - "y": 36.62, + "y": 29.06, "pos": 1 }, { "base": "G", "x": 74.57, - "y": 44.18, + "y": 36.62, "pos": 2 }, { "base": "C", "x": 74.78, - "y": 51.74, + "y": 44.18, "pos": 3 }, { "base": "C", "x": 74.78, - "y": 59.3, + "y": 51.74, "pos": 4 }, { "base": "G", "x": 74.57, - "y": 66.86, + "y": 59.3, "pos": 5 }, { "base": "G", "x": 74.57, - "y": 74.42, + "y": 66.86, "pos": 6 }, { "base": "U", "x": 74.78, - "y": 81.98, + "y": 74.42, "pos": 7 }, { "base": "U", "x": 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b/inst/extdata/structures/Homo_sapiens/tRNA-Ile-GAT.svg index 217b7cb6..a071723f 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Ile-GAT.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Ile-GAT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="176.717" + height="169.157" id="svg2403" xml:space="preserve"> tRNA-Ile-GAT + @@ -30,19 +33,19 @@ d="M 81.6597 71.7285 L 85.5477 71.7285 "/> + d="M 60.0967 88.2051 L 60.0967 92.0931 "/> + d="M 52.5367 88.2051 L 52.5367 92.0931 "/> + d="M 44.9767 88.2051 L 44.9767 92.0931 "/> + d="M 37.4167 88.2051 L 37.4167 92.0931 "/> + d="M 74.7728 106.74 L 78.6608 106.74 "/> @@ -57,251 +60,245 @@ d="M 74.7728 136.98 L 78.6608 136.98 "/> + d="M 95.0847 85.123 L 95.0847 81.235 "/> + d="M 102.645 85.123 L 102.645 81.235 "/> + d="M 110.205 85.123 L 110.205 81.235 "/> + d="M 117.765 85.123 L 117.765 81.235 "/> - - - G - - - G + d="M 125.325 85.123 L 125.325 81.235 "/> + + G - - C + + G - - C + + C - - 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a/inst/extdata/structures/Homo_sapiens/tRNA-Ile-TAT.json b/inst/extdata/structures/Homo_sapiens/tRNA-Ile-TAT.json index 557d5764..6f68937b 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Ile-TAT.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Ile-TAT.json @@ -3,452 +3,470 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 74.78, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "U", "x": 74.78, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "C", "x": 74.78, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 74.78, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "A", "x": 74.98, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "G", "x": 74.57, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 67.34, - "y": 106.05, + "y": 98.49, "pos": 8 }, { "base": "G", "x": 60.96, - "y": 110.42, + "y": 102.86, "pos": 9 }, { "base": "G", "x": 57.18, - "y": 116.96, + "y": 109.4, "pos": 10 }, { "base": "C", "x": 49.83, - "y": 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C - - U + + U - - C + + U - - G + + C - - G + + G - - A + + G - - G + + A - - G + + G - - C + + G - - G + + C - - U + + G - - G + + U - - G + + G - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - A + + A - - U + + A - - C + + U - - C + + C - - C + + C - - A + + C - - C + + A - - C + + C - - G + + C - - C + + G - - U + + C - - G + + U - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 22.8047 A 1.78191,1.78191 270 0,0 75.7018,21.0228L 72.138 21.0228 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAA.json b/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAA.json index 09206e8e..a8b94019 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAA.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAA.json @@ -3,506 +3,524 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "U", "x": 74.78, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 74.78, - "y": 74.42, + "y": 66.86, 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"<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.<<<<...>>>>..<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAA.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAA.svg index 79f529f8..bbff7cc8 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAA.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Leu-CAA + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,299 +60,293 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 91.7766 117.916 L 94.5258 115.166 "/> + d="M 97.1223 123.261 L 99.8715 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"<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.<<<<...>>>>..<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAG.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAG.svg index 10d3e5d9..0b1840c7 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAG.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Leu-CAG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Leu-CAG + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,299 +60,293 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 91.7766 117.916 L 94.5258 115.166 "/> + d="M 97.1223 123.261 L 99.8715 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"<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.<<<<....>>>>..<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Leu-TAA.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Leu-TAA.svg index c0da63bc..816da907 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Leu-TAA.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Leu-TAA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Leu-TAA + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,299 +60,293 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 88.7184 117.916 L 91.4676 115.166 "/> + d="M 94.0641 123.261 L 96.8134 120.512 "/> + d="M 99.4099 128.607 L 102.159 125.858 "/> + d="M 104.756 133.953 L 107.505 131.204 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 L 99.5865 103.915 "/> + d="M 107.146 107.803 L 107.146 103.915 "/> + d="M 114.706 107.803 L 114.706 103.915 "/> - - - A - - - C + d="M 122.266 107.803 L 122.266 103.915 "/> + + A - - C + + C - - A + + C - - G + + A - - G + + G - - A + + G - - U + + A - - G + + U - - G + + G - - C + + G - - C + + C - - G + + C - - A + + G - - G + + A - - U + + G - - G + + U - - G + + G - - U + + G - - U + + U - - A + + U - - A + + A - - G + + A - - G + + G - - C + + G - - G + + C - - U + + G - - U + + U - - G + + U - - G + + G - - A + + G - - C + + A - - U + + C - - U + + U - - A + + U - - A + + A - - G + + A - - A + + G - - U + + A - - C + + U - - C + + C - - A + + C - - A + + A - - U + + A - - G + + U - - G + + G - - A + + G - - C + + A - - A + + C - - U + + A - - A + + U - - U + + A - - G + + U - - U + + G - - C + + U - - C + + C - - G + + C - - C + + G - - G + + C - - U + + G - - G + + U - - G + + G - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - A + + A - - C + + A - - C + + C - - C + + C - - C + + C - - A + + C - - C + + A - - U + + C - - C + + U - - C + + C - - U + + C - - G + + U - - G + + G - - U + + G - - A + + U - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Leu-TAG.json b/inst/extdata/structures/Homo_sapiens/tRNA-Leu-TAG.json index 5f7f8658..0e57e9d3 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Leu-TAG.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Leu-TAG.json @@ -3,500 +3,500 @@ { "base": "G", "x": 74.57, - "y": 36.62, + "y": 29.06, "pos": 1 }, { "base": "G", "x": 74.57, - "y": 44.18, + "y": 36.62, "pos": 2 }, { "base": "U", "x": 74.78, - "y": 51.74, + "y": 44.18, "pos": 3 }, { "base": "A", "x": 74.98, - 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18778405..196c1356 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Lys-TTT.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Lys-TTT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.253" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Lys-TTT + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 "/> + d="M 99.5865 107.803 L 99.5865 103.915 "/> + d="M 107.146 107.803 L 107.146 103.915 "/> + d="M 114.706 107.803 L 114.706 103.915 "/> - - - G - - - C + d="M 122.266 107.803 L 122.266 103.915 "/> + + G - - C + + C - - U + + C - - G + + U - - G + + G - - A + + G - - U + + A - - A + 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b/inst/extdata/structures/Homo_sapiens/tRNA-Met-CAT.json index a7a888dd..3fec0d7b 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Met-CAT.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Met-CAT.json @@ -3,446 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 71.72, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 71.72, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "G", "x": 71.51, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "U", "x": 71.72, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 64.29, - "y": 106.05, + "y": 98.49, "pos": 8 }, { "base": "A", "x": 58.32, - "y": 110.42, + "y": 102.86, "pos": 9 }, { "base": "G", "x": 54.12, - "y": 116.96, + "y": 109.4, "pos": 10 }, { "base": "C", "x": 46.77, - "y": 116.96, + "y": 109.4, "pos": 11 }, { "base": "G", "x": 39.0, - 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"<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.<<<<...>>>>..<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Ser-TGA.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Ser-TGA.svg index 84157d66..a2544a7f 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Ser-TGA.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Ser-TGA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Ser-TGA + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,296 +60,290 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 88.7184 117.916 L 91.4676 115.166 "/> + d="M 94.0641 123.261 L 96.8134 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C + + G - - G + + C - - C + + G - - A + + C - - G + + A - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - A + + A - - C + + A - - C + + C - - C + + C - - U + + C - - G + + U - - C + + G - - U + + C - - C + + U - - G + + C - - C + + G - - U + + C - - G + + U - - C + + G - - G + + C - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Thr-AGT.json b/inst/extdata/structures/Homo_sapiens/tRNA-Thr-AGT.json index 374e9586..5aaf7c5f 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Thr-AGT.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Thr-AGT.json @@ -3,452 +3,470 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 74.57, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 74.78, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 74.57, - "y": 81.98, + 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47 }, { "base": "U", "x": 101.71, - "y": 133.07, + "y": 125.51, "pos": 48 }, { "base": "C", "x": 98.9, - "y": 126.05, + "y": 118.49, "pos": 49 }, { "base": "C", "x": 92.38, - "y": 122.23, + "y": 114.67, "pos": 50 }, { "base": "U", "x": 99.94, - "y": 122.23, + "y": 114.67, "pos": 51 }, { "base": "G", "x": 107.29, - "y": 122.23, + "y": 114.67, "pos": 52 }, { "base": "G", "x": 114.85, - "y": 122.23, + "y": 114.67, "pos": 53 }, { "base": "G", "x": 122.41, - "y": 122.23, + "y": 114.67, "pos": 54 }, { "base": "U", "x": 128.38, - "y": 127.12, + "y": 119.56, "pos": 55 }, { "base": "U", "x": 135.93, - "y": 127.52, + "y": 119.96, "pos": 56 }, { "base": "C", "x": 142.19, - "y": 123.28, + "y": 115.72, "pos": 57 }, { "base": "G", "x": 144.39, - "y": 116.11, + "y": 108.55, "pos": 58 }, { "base": "A", "x": 142.4, - "y": 108.95, + "y": 101.39, "pos": 59 }, { "base": "A", "x": 136.14, - "y": 104.7, + "y": 97.14, "pos": 60 }, { "base": "U", "x": 128.38, - "y": 105.1, + "y": 97.54, "pos": 61 }, { "base": "C", "x": 122.62, - "y": 109.99, + "y": 102.43, "pos": 62 }, { "base": "C", "x": 115.06, - "y": 109.99, + "y": 102.43, "pos": 63 }, { "base": "C", "x": 107.5, - "y": 109.99, + "y": 102.43, "pos": 64 }, { "base": "A", "x": 100.14, - "y": 109.99, + "y": 102.43, "pos": 65 }, { "base": "G", "x": 92.17, - "y": 109.99, + "y": 102.43, "pos": 66 }, { "base": "C", "x": 87.02, - "y": 104.66, + "y": 97.1, "pos": 67 }, { "base": "G", "x": 86.81, - "y": 97.1, + "y": 89.54, "pos": 68 }, { "base": "G", "x": 86.81, - "y": 89.54, + "y": 81.98, "pos": 69 }, { "base": "U", "x": 87.02, - "y": 81.98, + "y": 74.42, "pos": 70 }, { "base": "G", "x": 86.81, - "y": 74.42, + "y": 66.86, "pos": 71 }, { "base": "C", "x": 87.02, - "y": 66.86, + "y": 59.3, "pos": 72 }, { "base": "C", "x": 87.02, - "y": 59.3, + "y": 51.74, "pos": 73 }, { "base": "U", "x": 87.02, - "y": 51.74, + "y": 44.18, "pos": 74 + }, + { + "base": "C", + "x": 87.02, + "y": 36.62, + "pos": 75 + }, + { + "base": "C", + "x": 87.02, + "y": 29.06, + "pos": 76 + }, + { + "base": "A", + "x": 87.22, + "y": 21.5, + "pos": 77 } ], "width": 157.73, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Thr-AGT", "sequence": "GGCGCCGUGGCUUAGUUGGUUAAAGCGCCUGUCUAGUAAACAGGAGAUCCUGGGUUCGAAUCCCAGCGGUGCCU", "structure": "<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Thr-AGT.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Thr-AGT.svg index 3970a42d..6989ed65 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Thr-AGT.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Thr-AGT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Thr-AGT + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,260 +60,254 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 95.0847 107.803 L 95.0847 103.915 "/> + d="M 102.645 107.803 L 102.645 103.915 "/> + d="M 110.205 107.803 L 110.205 103.915 "/> + d="M 117.765 107.803 L 117.765 103.915 "/> - - - G - - - G + d="M 125.325 107.803 L 125.325 103.915 "/> + + G - - C + + G - - G + + C - - C + + G - - C + + C - - G + + C - - U + + G - - G + + U - - G + + G - - C + + G - - U + + C - - U + + U - - A + + U - - G + + A - - U + + G - - U + + U - - G + + U - - G + + G - - U + + G - - U + + U - - A + + U - - A + + A - - A + + A - - G + + A - - C + + G - - G + + C - - C + + G - - C + + C - - U + + C - - G + + U - - U + + G - - C + + U - - U + + C - - A + + U - - G + + A - - U + + G - - A + + U - - A + + A - - A + + A - - C + + A - - A + + C - - G + + A - - G + + G - - A + + G - - G + + A - - A + + G - - U + + A - - C + + U - - C + + C - - U + + C - - G + + U - - G + + G - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - A + + A - - U + + A - - C + + U - - C + + C - - C + + C - - A + + C - - G + + A - - C + + G - - G + + C - - G + + G - - U + + G - - G + + U - - C + + G - - C + + C - - U + + C - - C + + U - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 45.4847 A 1.78191,1.78191 270 0,0 75.7018,43.7028L 72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Thr-CGT.json b/inst/extdata/structures/Homo_sapiens/tRNA-Thr-CGT.json index 45bebf3f..6da4706a 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Thr-CGT.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Thr-CGT.json @@ -3,452 +3,470 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 74.57, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 74.78, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 74.78, - "y": 81.98, + "y": 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"trna_name": "tRNA-Trp-CCA", "sequence": "GGCCUCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA", "structure": "<<<<<<<..<<<<.......>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Trp-CCA.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Trp-CCA.svg index c1ae0479..8a267329 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Trp-CCA.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Trp-CCA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="152.296" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Trp-CCA + @@ -30,19 +33,19 @@ d="M 76.6454 94.4085 L 80.5334 94.4085 "/> + d="M 55.0824 110.885 L 55.0824 114.773 "/> + d="M 47.5224 110.885 L 47.5224 114.773 "/> + d="M 39.9624 110.885 L 39.9624 114.773 "/> + d="M 32.4024 110.885 L 32.4024 114.773 "/> + d="M 69.7584 129.42 L 73.6464 129.42 "/> @@ -57,254 +60,248 @@ 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"CCUUCAAUAGUUCAGCUGGUAGAGCAGAGGACUAUAGGUCCUUAGGUUGCUGGUUCGAUUCCAGCUUGAAGGA", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Tyr-ATA.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Tyr-ATA.svg index 6adfc982..c3d13264 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Tyr-ATA.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Tyr-ATA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Tyr-ATA + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 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"CCUUCGAUAGCUCAGUUGGUAGAGCGGAGGACUGUAGAUCCUUAGGUCGCUGGUUCGAAUCCGGCUCGAAGGA", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Tyr-GTA.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Tyr-GTA.svg index b4e604b8..5e4a2152 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Tyr-GTA.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Tyr-GTA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Tyr-GTA + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 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+ + G - - U + + C - - C + + U - - G + + C - - A + + G - - A + + A - - G + + A - - G + + G - - A + + G - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Val-AAC.json b/inst/extdata/structures/Homo_sapiens/tRNA-Val-AAC.json index d2cb717e..db8373b7 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Val-AAC.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Val-AAC.json @@ -3,446 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "U", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "U", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 71.72, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 71.72, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "C", "x": 71.72, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "G", "x": 71.51, - "y": 104.66, + "y": 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+ + G - - C + + G - - G + + C - - G + + G - - A + + G - - A + + A - - A + + A - - C + + A - - A + + C - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Val-CAC.json b/inst/extdata/structures/Homo_sapiens/tRNA-Val-CAC.json index 586e52df..266b9edb 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Val-CAC.json +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Val-CAC.json @@ -3,446 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "U", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "U", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 71.72, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 71.72, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "C", "x": 71.72, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "G", "x": 71.51, - "y": 104.66, + "y": 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"GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Homo_sapiens/tRNA-Val-CAC.svg b/inst/extdata/structures/Homo_sapiens/tRNA-Val-CAC.svg index cfc37f2e..23f78bfd 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Val-CAC.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Val-CAC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Val-CAC + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,257 +60,251 @@ d="M 71.7146 159.66 L 75.6026 159.66 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b/inst/extdata/structures/Homo_sapiens/tRNA-Val-TAC.svg index 8c33c84c..29e64892 100644 --- a/inst/extdata/structures/Homo_sapiens/tRNA-Val-TAC.svg +++ b/inst/extdata/structures/Homo_sapiens/tRNA-Val-TAC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="176.717" + height="169.157" id="svg2403" xml:space="preserve"> tRNA-Val-TAC + @@ -30,19 +33,19 @@ d="M 78.6015 71.7285 L 82.4895 71.7285 "/> + d="M 57.0385 88.2051 L 57.0385 92.0931 "/> + d="M 49.4785 88.2051 L 49.4785 92.0931 "/> + d="M 41.9185 88.2051 L 41.9185 92.0931 "/> + d="M 34.3585 88.2051 L 34.3585 92.0931 "/> + d="M 71.7146 106.74 L 75.6026 106.74 "/> @@ -57,248 +60,242 @@ d="M 71.7146 136.98 L 75.6026 136.98 "/> + d="M 92.0265 85.123 L 92.0265 81.235 "/> + d="M 99.5865 85.123 L 99.5865 81.235 "/> + d="M 107.146 85.123 L 107.146 81.235 "/> + d="M 114.706 85.123 L 114.706 81.235 "/> - - - G - - - G + d="M 122.266 85.123 L 122.266 81.235 "/> + + G - - U + + G - - U + + U - - C + + U - - C + + C - - A + + C - - U + + A - - A + + U - - G + + A - - U + + G - - G + + U - - U + + G - - A + + U - - G + + A - - U + + G - - G + + U - - G + + G - - U + + G - - U + + U - - A + + U - - U + + A - - C + + U - - A + + C - - C + + A - - G + + C - - U + + G - - C + + U - - U + + C - - G + + U - - C + + G - - U + + C - - U + + U - - U + + U - - A + + U - - C + + A - - A + + C - - C + + A - - G + + C - - C + + G - - A + + C - - G + + A - - A + + G - - A + + A - - G + + A - - G + + G - - U + + G - - C + + U - - C + + C - - U + + C - - G + + U - - G + + G - - G + + G - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - G + + A - - C + + G - - C + + C - - C + + C - - C + + C - - A + + C - - G + + A - - U + + G - - G + + U - - G + + G - - A + + G - - A + + A - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 22.8047 A 1.78191,1.78191 270 0,0 72.6436,21.0228L 69.0798 21.0228 "/> + + 5' diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Ala-AGC.json b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Ala-AGC.json index 91a06f63..92685a94 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Ala-AGC.json +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Ala-AGC.json @@ -3,446 +3,446 @@ { "base": "G", "x": 71.51, - "y": 36.62, + "y": 29.06, "pos": 1 }, { "base": "G", "x": 71.51, - "y": 44.18, + "y": 36.62, "pos": 2 }, { "base": "G", "x": 71.51, - "y": 51.74, + "y": 44.18, "pos": 3 }, { "base": "C", "x": 71.72, - "y": 59.3, + "y": 51.74, "pos": 4 }, { "base": "G", "x": 71.51, - "y": 66.86, + "y": 59.3, "pos": 5 }, { "base": "U", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 6 }, { "base": "G", "x": 71.51, - "y": 81.98, + "y": 74.42, "pos": 7 }, { "base": "U", "x": 64.29, - "y": 83.37, + "y": 75.81, "pos": 8 }, { "base": "G", "x": 57.91, - "y": 87.74, + "y": 80.18, "pos": 9 }, { "base": "G", "x": 54.12, - "y": 94.28, + "y": 86.72, "pos": 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-4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="176.717" + height="169.157" id="svg2403" xml:space="preserve"> tRNA-Ala-AGC + @@ -30,19 +33,19 @@ d="M 78.6015 71.7285 L 82.4895 71.7285 "/> + d="M 57.0385 88.2051 L 57.0385 92.0931 "/> + d="M 49.4785 88.2051 L 49.4785 92.0931 "/> + d="M 41.9185 88.2051 L 41.9185 92.0931 "/> + d="M 34.3585 88.2051 L 34.3585 92.0931 "/> + d="M 71.7146 106.74 L 75.6026 106.74 "/> @@ -57,248 +60,242 @@ d="M 71.7146 136.98 L 75.6026 136.98 "/> + d="M 92.0265 85.123 L 92.0265 81.235 "/> + d="M 99.5865 85.123 L 99.5865 81.235 "/> + d="M 107.146 85.123 L 107.146 81.235 "/> + d="M 114.706 85.123 L 114.706 81.235 "/> - - - G - - - G + d="M 122.266 85.123 L 122.266 81.235 "/> + + G - - G + + G - - C + + G - - G + + C - - U + + G - - G + + U - - U + + G - - G + + U - - G + + G - - C + + G - - G + + C - - U + + G - - A + + U - - G + + A - - U + + G - - C + + U - - G + + C - - G + + G - - U + + G - - A + + U - - G + + 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83.96, - "y": 36.62, + "y": 29.06, "pos": 72 }, { "base": "A", "x": 84.16, - "y": 29.06, + "y": 21.5, "pos": 73 } ], "width": 154.67, - "height": 176.72, + "height": 169.16, "lines": [], "trna_name": "tRNA-Ala-TGC", "sequence": "GGGCACAUGGCGCAGUUGGUAGCGCGCUUCCCUUGCAAGGAAGAGGUCAUCGGUUCGAUUCCGGUUGCGUCCA", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Ala-TGC.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Ala-TGC.svg index ba8b5bb3..93a009c2 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Ala-TGC.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Ala-TGC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="176.717" + height="169.157" id="svg2403" xml:space="preserve"> tRNA-Ala-TGC + @@ -30,19 +33,19 @@ d="M 78.6015 71.7285 L 82.4895 71.7285 "/> + d="M 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29.06, + "pos": 75 + }, + { + "base": "A", + "x": 84.16, + "y": 21.5, + "pos": 76 } ], "width": 154.25, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Arg-ACG", "sequence": "UUCCUCGUGGCCCAAUGGUCACGGCGUCUGGCUACGAACCAGAAGAUUCCAGGUUCAAGUCCUGGCGGGGAAG", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Arg-ACG.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Arg-ACG.svg index a1e159ea..a5660b84 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Arg-ACG.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Arg-ACG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.253" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Arg-ACG + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 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"GCUCGCGUGGCGUAAUGGCAACGCGUCUGACUUCUAAUCAGAAGAUUAUGGGUUCGACCCCCAUCGUGAGUG", "structure": "<<<<<<<..<<<<.......>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Arg-TCT.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Arg-TCT.svg index d7844a94..01402983 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Arg-TCT.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Arg-TCT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="152.713" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Arg-TCT + @@ -30,19 +33,19 @@ d="M 76.6454 94.4085 L 80.5334 94.4085 "/> + d="M 55.0824 110.885 L 55.0824 114.773 "/> + d="M 47.5224 110.885 L 47.5224 114.773 "/> + d="M 39.9624 110.885 L 39.9624 114.773 "/> + d="M 32.4024 110.885 L 32.4024 114.773 "/> + d="M 69.7584 129.42 L 73.6464 129.42 "/> @@ -57,254 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- - C + + C - - A + + C - - U + + A - - C + + U - - G + + C - - U + + G - - G + + U - - A + + G - - G + + A - - U + + G - - G + + U - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 72.4694 45.4847 A 1.78191,1.78191 270 0,0 70.6875,43.7028L 67.1236 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asn-GTT.json b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asn-GTT.json index 31748333..5eb909f8 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asn-GTT.json +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asn-GTT.json @@ -3,452 +3,470 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "A", "x": 74.98, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 74.78, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "U", "x": 74.78, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 74.78, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "C", "x": 74.78, - "y": 97.1, 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"height": 191.84, "lines": [], "trna_name": "tRNA-Asn-GTT", "sequence": "GACUCCAUGGCCAAGUUGGUUAAGGCGUGCGACUGUUAAUCGCAAGAUCGUGAGUUCAACCCUCACUGGGGUCG", "structure": "<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asn-GTT.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asn-GTT.svg index b76b3206..97880525 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asn-GTT.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asn-GTT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.311" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Asn-GTT + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,260 +60,254 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 95.0847 107.803 L 95.0847 103.915 "/> + d="M 102.645 107.803 L 102.645 103.915 "/> + d="M 110.205 107.803 L 110.205 103.915 "/> + d="M 117.765 107.803 L 117.765 103.915 "/> - - - G - - - A + d="M 125.325 107.803 L 125.325 103.915 "/> + + G - - C + + A - - U + + C - - C + + U - - C + + C - - A + + C - - U + + A - - G + + U - - G + + G - - C + + G - - C + + C - - A + + C - - A + + A - - G + + A - - U + + G - - U + + U - - G + + U - - G + + G - - U + + G - - U + + U - - A + + U - - A + + A - - G + + A - - G + + G - - C + + G - - G + + C - - U + + G - - G + + U - - C + + G - - G + + C - - A + + G - - C + + A - - U + + C - - G + + U - - U + + G - - U + + U - - A + + U - - A + + A - - U + + A - - C + + U - - G + + C - - C + + G - - A + + C - - A + + A - - G + + A - - A + + G - - U + + A - - C + + U - - G + + C - - U + + G - - G + + U - - A + + G - - G + + A - - U + + G - - U + + U - - C + + U - - A + + C - - A + + A - - C + + A - - C + + C - - C + + C - - U + + C - - C + + U - - A + + C - - C + + A - - U + + C - - G + + U - - G + + G - - G + + G - - G + + G - - U + + G - - C + + U - - G + + C - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 45.4847 A 1.78191,1.78191 270 0,0 75.7018,43.7028L 72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asp-GTC.json b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asp-GTC.json index b803006c..b5442ecd 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asp-GTC.json +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asp-GTC.json @@ -3,440 +3,458 @@ { "base": "U", "x": 71.72, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 71.51, - "y": 81.98, + "y": 74.42, "pos": 4 }, { 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"tRNA-Asp-GTC", "sequence": "UCCGUGAUAGUUUAAUGGUCAGAAUGGGCGCUUGUCGCGUGCCAGAUCGGGGUUCAAUUCCCCGUCGCGGAG", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asp-GTC.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asp-GTC.svg index e32efa0b..739ced4f 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asp-GTC.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Asp-GTC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.253" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Asp-GTC + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 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- - U + + U - - C + + U - - C + + C - - C + + C - - C + + C - - G + + C - - U + + G - - C + + U - - G + + C - - C + + G - - G + + C - - G + + G - - A + + G - - G + + A - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Cys-GCA.json b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Cys-GCA.json index 4e9db097..1caec626 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Cys-GCA.json +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Cys-GCA.json @@ -3,440 +3,458 @@ { "base": "G", "x": 69.55, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 69.76, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "U", "x": 69.76, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "C", "x": 69.76, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "G", "x": 69.55, - "y": 89.54, + "y": 81.98, "pos": 5 }, { 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"GCUCGUAUGGCGCAGUGGUAGCGCAGCAGAUUGCAAAUCUGUUGGUCCUUAGUUCGAUCCUGAGUGCGAGCU", "structure": "<<<<<<<..<<<<.......>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Cys-GCA.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Cys-GCA.svg index 49c1a8d3..0cfeb62d 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Cys-GCA.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Cys-GCA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="152.713" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Cys-GCA + @@ -30,19 +33,19 @@ d="M 76.6454 94.4085 L 80.5334 94.4085 "/> + d="M 55.0824 110.885 L 55.0824 114.773 "/> + d="M 47.5224 110.885 L 47.5224 114.773 "/> + d="M 39.9624 110.885 L 39.9624 114.773 "/> + d="M 32.4024 110.885 L 32.4024 114.773 "/> + d="M 69.7584 129.42 L 73.6464 129.42 "/> @@ -57,254 +60,248 @@ d="M 69.7584 159.66 L 73.6464 159.66 "/> + d="M 90.0703 107.803 L 90.0703 103.915 "/> + d="M 97.6303 107.803 L 97.6303 103.915 "/> + d="M 105.19 107.803 L 105.19 103.915 "/> + d="M 112.75 107.803 L 112.75 103.915 "/> - - - G - - - C + d="M 120.31 107.803 L 120.31 103.915 "/> + + G - - U + + C - - C + + U - - G + + C - - U + + G - - A + + U - - U + + A - - G + + U - - G + + G - - C + + G - - G + + C - - C + + G - - A + + C - - G + + A - - U + + G - - G + + U - - G + + G - - U + + G - - A + + U - - G + + A - - C + + G - - G + + C - - C + + G - - A + + C - - G + + A - - C + + G - - A + + C - - G + + A - - A + + G - - U + + A - - U + + U - - G + + U - - C + + G - - A + + C - - A + + A - - A + + A - - U + + A - - C + + U - - U + + C - - G + + U - - U + + G - - U + + U - - G + + U - - G + + G - - U + + G - - C + + U - - C + + C - - U + + C - - U + + U - - A + + U - - G + + A - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - U + + A - - C + + U - - C + + C - - U + + C - - G + + U - - A + + G - - G + + A - - U + + G - - G + + U - - C + + G - - G + + C - - A + + G - - G + + A - - C + + G - - U + + C - - C + + U - - C + + C - - A + + C - - A + + A - - 5' + d="M 72.4694 45.4847 A 1.78191,1.78191 270 0,0 70.6875,43.7028L 67.1236 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-CTC.json b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-CTC.json index 44d41b98..6258704a 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-CTC.json +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-CTC.json @@ -3,440 +3,458 @@ { "base": "U", "x": 71.72, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 71.51, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "A", "x": 71.92, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "U", "x": 71.72, - "y": 97.1, 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{ "base": "G", "x": 89.11, - "y": 109.99, + "y": 102.43, "pos": 64 }, { "base": "C", "x": 83.96, - "y": 104.66, + "y": 97.1, "pos": 65 }, { "base": "U", "x": 83.96, - "y": 97.1, + "y": 89.54, "pos": 66 }, { "base": "U", "x": 83.96, - "y": 89.54, + "y": 81.98, "pos": 67 }, { "base": "C", "x": 83.96, - "y": 81.98, + "y": 74.42, "pos": 68 }, { "base": "G", "x": 83.75, - "y": 74.42, + "y": 66.86, "pos": 69 }, { "base": "G", "x": 83.75, - "y": 66.86, + "y": 59.3, "pos": 70 }, { "base": "A", "x": 84.16, - "y": 59.3, + "y": 51.74, "pos": 71 }, { "base": "G", "x": 83.75, - "y": 51.74, + "y": 44.18, "pos": 72 + }, + { + "base": "C", + "x": 83.96, + "y": 36.62, + "pos": 73 + }, + { + "base": "C", + "x": 83.96, + "y": 29.06, + "pos": 74 + }, + { + "base": "A", + "x": 84.16, + "y": 21.5, + "pos": 75 } ], "width": 154.67, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Glu-CTC", "sequence": "UCCGAUGUAGUGUAACGGCUAUCACAUCACGUUCUCACCGUGGAGACCGGGGUUCGACUCCCCGCUUCGGAG", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-CTC.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-CTC.svg index f559c588..eb9824ea 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-CTC.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-CTC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Glu-CTC + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,254 +60,248 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 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U - - C + + U - - G + + C - - G + + G - - A + + G - - G + + A - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-TTC.json b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-TTC.json index 004ee6ff..3713c538 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-TTC.json +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-TTC.json @@ -3,440 +3,458 @@ { "base": "U", "x": 71.72, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "C", "x": 71.72, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 71.51, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "A", "x": 71.92, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "U", "x": 71.72, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "A", "x": 71.92, - "y": 104.66, + 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"<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-TTC.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-TTC.svg index 12b615bf..469f401e 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-TTC.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Glu-TTC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Glu-TTC + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,254 +60,248 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 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- G + + C - - G + + G - - A + + G - - G + + A - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Gly-CCC.json b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Gly-CCC.json index 04038922..4a5aab77 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Gly-CCC.json +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Gly-CCC.json @@ -3,440 +3,458 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "G", "x": 71.51, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "C", "x": 71.72, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "A", "x": 71.92, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "A", "x": 71.92, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "G", "x": 71.51, - "y": 104.66, + "y": 97.1, 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"<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Gly-CCC.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Gly-CCC.svg index a25c343b..e7ad8ccb 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Gly-CCC.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Gly-CCC.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Gly-CCC + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 "/> @@ -57,254 +60,248 @@ d="M 71.7146 159.66 L 75.6026 159.66 "/> + d="M 92.0265 107.803 L 92.0265 103.915 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"GGUUGUUUGGCCGAGCGGUCUAAGGCGCCUGAUUCAAGCUCAGGUAUCGUAAGAUGCAAGAGUUCGAAUCUCUUAGCAACCA", "structure": "<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.<<<....>>>..<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-CAA.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-CAA.svg index bc04113f..0820a0c9 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-CAA.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-CAA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="176.717" + height="169.157" id="svg2403" xml:space="preserve"> tRNA-Leu-CAA + @@ -30,19 +33,19 @@ d="M 81.6597 71.7285 L 85.5477 71.7285 "/> + d="M 60.0967 88.2051 L 60.0967 92.0931 "/> + d="M 52.5367 88.2051 L 52.5367 92.0931 "/> + d="M 44.9767 88.2051 L 44.9767 92.0931 "/> + d="M 37.4167 88.2051 L 37.4167 92.0931 "/> + d="M 74.7728 106.74 L 78.6608 106.74 "/> @@ -57,284 +60,278 @@ d="M 74.7728 136.98 L 78.6608 136.98 "/> + d="M 91.7766 95.2356 L 94.5258 92.4864 "/> + d="M 97.1223 100.581 L 99.8715 97.8321 "/> + d="M 102.468 105.927 L 105.217 103.178 "/> + d="M 95.0847 85.123 L 95.0847 81.235 "/> + d="M 102.645 85.123 L 102.645 81.235 "/> + d="M 110.205 85.123 L 110.205 81.235 "/> + d="M 117.765 85.123 L 117.765 81.235 "/> - - - G - - - G + d="M 125.325 85.123 L 125.325 81.235 "/> + + G - - U + + G - - U + + U - - G + + U - - U + + G - - U + + U - - U + + U - - G + + U - - G + + G - - C + + G - - C + + C - - G + + C - - A + + G - - G + + A - - C + + G - - G + + C - - G + + G - - U + + G - - C + + U - - U + + C - - A + + U - - A + + A - - G + + A - - G + + G - - C + + G - - G + + C - - C + + G - - C + + C - - U + + C - - G + + U - - A + + G - - U + + A - - U + + U - - C + + U - - A + + C - - A + + A - - G + + A - - C + + G - - U + + C - - C + + U - - A + + C - - G + + A - - G + + G - - U + + G - - A + + U - - U + + A - - C + + U - - G + + C - - U + + G - - A + + U - - A + + A - - G + + A - - A + + G - - U + + A - - G + + U - - C + + G - - A + + C - - A + + A - - G + + A - - A + + G - - G + + A - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - A + + A - - U + + A - - C + + U - - U + + C - - C + + U - - U + + C - - U + + U - - A + + U - - G + + A - - C + + G - - A + + C - - A + + A - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 22.8047 A 1.78191,1.78191 270 0,0 75.7018,21.0228L 72.138 21.0228 "/> + + 5' diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-GAG.json b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-GAG.json index 01fba062..7f3ae9a3 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-GAG.json +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-GAG.json @@ -3,500 +3,518 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 74.57, - "y": 66.86, + "y": 59.3, "pos": 2 }, { 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+ "y": 114.67, "pos": 60 }, { "base": "G", "x": 114.85, - "y": 122.23, + "y": 114.67, "pos": 61 }, { "base": "G", "x": 122.41, - "y": 122.23, + "y": 114.67, "pos": 62 }, { "base": "U", "x": 128.38, - "y": 127.12, + "y": 119.56, "pos": 63 }, { "base": "U", "x": 135.93, - "y": 127.52, + "y": 119.96, "pos": 64 }, { "base": "C", "x": 142.19, - "y": 123.28, + "y": 115.72, "pos": 65 }, { "base": "A", "x": 144.81, - "y": 116.11, + "y": 108.55, "pos": 66 }, { "base": "A", "x": 142.4, - "y": 108.95, + "y": 101.39, "pos": 67 }, { "base": "A", "x": 136.14, - "y": 104.7, + "y": 97.14, "pos": 68 }, { "base": "C", "x": 128.38, - "y": 105.1, + "y": 97.54, "pos": 69 }, { "base": "C", "x": 122.62, - "y": 109.99, + "y": 102.43, "pos": 70 }, { "base": "C", "x": 115.06, - "y": 109.99, + "y": 102.43, "pos": 71 }, { "base": "C", "x": 107.5, - "y": 109.99, + "y": 102.43, "pos": 72 }, { "base": "G", "x": 99.73, - "y": 109.99, + "y": 102.43, "pos": 73 }, { "base": "C", "x": 92.38, - "y": 109.99, + "y": 102.43, 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"<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.<<<....>>>..<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-GAG.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-GAG.svg index 27fef3d2..a72513f1 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-GAG.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Leu-GAG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.311" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Leu-GAG + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,293 +60,287 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 91.7766 117.916 L 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89.54, "pos": 76 }, { "base": "G", "x": 83.75, - "y": 89.54, + "y": 81.98, "pos": 77 }, { "base": "U", "x": 83.96, - "y": 81.98, + "y": 74.42, "pos": 78 }, { "base": "G", "x": 83.75, - "y": 74.42, + "y": 66.86, "pos": 79 }, { "base": "U", "x": 83.96, - "y": 66.86, + "y": 59.3, "pos": 80 }, { "base": "C", "x": 83.96, - "y": 59.3, + "y": 51.74, "pos": 81 }, { "base": "G", "x": 83.75, - "y": 51.74, + "y": 44.18, "pos": 82 + }, + { + "base": "C", + "x": 83.96, + "y": 36.62, + "pos": 83 + }, + { + "base": "C", + "x": 83.96, + "y": 29.06, + "pos": 84 + }, + { + "base": "A", + "x": 84.16, + "y": 21.5, + "pos": 85 } ], "width": 154.25, - "height": 199.4, + "height": 191.84, "lines": [], "trna_name": "tRNA-Ser-TGA", "sequence": "GGCACUAUGGCCGAGUGGUUAAGGCGACAGACUUGAAAUCUGUUGGGCUCUGCCCGCGCUGGUUCAAAUCCUGCUGGUGUCG", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.<<<<...>>>>..<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git 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"trna_name": "tRNA-Thr-CGT", "sequence": "GCCCUUUUGGCCAAGUGGUAAGGCAUCGCACUCGUAAUGCGGGGAUCGUGGGUUCAAUUCCCACAGAGGGCA", "structure": "<<<<<<<..<<<<.......>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Thr-CGT.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Thr-CGT.svg index 9ec6f192..70138a9d 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Thr-CGT.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Thr-CGT.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="152.296" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Thr-CGT + @@ -30,19 +33,19 @@ d="M 76.6454 94.4085 L 80.5334 94.4085 "/> + d="M 55.0824 110.885 L 55.0824 114.773 "/> + d="M 47.5224 110.885 L 47.5224 114.773 "/> + d="M 39.9624 110.885 L 39.9624 114.773 "/> + d="M 32.4024 110.885 L 32.4024 114.773 "/> + d="M 69.7584 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- - G + + U - - G + + G - - C + + G - - A + + C - - G + + A - - G + + G - - U + + G - - G + + U - - G + + G - - C + + G - - A + + C - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 72.4694 45.4847 A 1.78191,1.78191 270 0,0 70.6875,43.7028L 67.1236 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Trp-CCA.json b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Trp-CCA.json index 0441405f..f73f1743 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Trp-CCA.json +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Trp-CCA.json @@ -3,440 +3,458 @@ { "base": "G", "x": 69.55, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "A", "x": 69.97, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "A", "x": 69.97, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 69.55, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "C", "x": 69.76, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "G", "x": 69.55, - "y": 97.1, 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"structure": "<<<<<<<..<<<<.......>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Trp-CCA.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Trp-CCA.svg index 14f7d109..689749e7 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Trp-CCA.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Trp-CCA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="152.296" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Trp-CCA + @@ -30,19 +33,19 @@ d="M 76.6454 94.4085 L 80.5334 94.4085 "/> + d="M 55.0824 110.885 L 55.0824 114.773 "/> + d="M 47.5224 110.885 L 47.5224 114.773 "/> + d="M 39.9624 110.885 L 39.9624 114.773 "/> + d="M 32.4024 110.885 L 32.4024 114.773 "/> + d="M 69.7584 129.42 L 73.6464 129.42 "/> @@ -57,254 +60,248 @@ d="M 69.7584 159.66 L 73.6464 159.66 "/> + d="M 90.0703 107.803 L 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"lines": [], "trna_name": "tRNA-Tyr-GTA", "sequence": "CUCUCGGUAGCCAAGUUGGUUUAAGGCGCAAGACUGUAAAUCUUGAGAUCGGGCGUUCGACUCGCCCCCGGGAGA", "structure": "<<<<<<<..<<<<..........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Tyr-GTA.svg b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Tyr-GTA.svg index b4c257d9..4d1474d4 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Tyr-GTA.svg +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Tyr-GTA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="159.737" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Tyr-GTA + @@ -30,19 +33,19 @@ d="M 83.6701 94.4085 L 87.5581 94.4085 "/> + d="M 62.1071 110.885 L 62.1071 114.773 "/> + d="M 54.5471 110.885 L 54.5471 114.773 "/> + d="M 46.9871 110.885 L 46.9871 114.773 "/> + d="M 39.4271 110.885 L 39.4271 114.773 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- - G + + C - - U + + G - - C + + U - - C + + C - - C + + C - - C + + C - - A + + C - - G + + A - - U + + G - - U + + U - - C + + U - - G + + C - - A + + G - - U + + A - - C + + U - - C + + C - - U + + C - - G + + U - - G + + G - - G + + G - - C + + G - - G + + C - - A + + G - - A + + A - - A + + A - - U + + A - - C + + U - - A + + C - - C + + A - - C + + C - - A + + C - - A + + A - - 5' + d="M 77.4837 45.4847 A 1.78191,1.78191 270 0,0 75.7018,43.7028L 72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Val-CAC.json b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Val-CAC.json index d2769a1e..a04b543c 100644 --- a/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Val-CAC.json +++ b/inst/extdata/structures/Saccharomyces_cerevisiae/tRNA-Val-CAC.json @@ -3,446 +3,464 @@ { "base": "G", "x": 71.51, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "U", "x": 71.72, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "U", "x": 71.72, - "y": 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"height": 191.84, "lines": [], "trna_name": "tRNA-Gln-TTG", "sequence": "UGGGAAUUAGCCAAGUUGGUAAGGCAUAGCACUUUGACUGCUAGAUGCAAAGGUUCGAGUCCUUUAUUCCCAGCCA", "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/T4_phage/tRNA-Gln-TTG.svg b/inst/extdata/structures/T4_phage/tRNA-Gln-TTG.svg index a19caae6..42ba39f9 100644 --- a/inst/extdata/structures/T4_phage/tRNA-Gln-TTG.svg +++ b/inst/extdata/structures/T4_phage/tRNA-Gln-TTG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="154.669" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Gln-TTG + @@ -30,19 +33,19 @@ d="M 78.6015 94.4085 L 82.4895 94.4085 "/> + d="M 57.0385 110.885 L 57.0385 114.773 "/> + d="M 49.4785 110.885 L 49.4785 114.773 "/> + d="M 41.9185 110.885 L 41.9185 114.773 "/> + d="M 34.3585 110.885 L 34.3585 114.773 "/> + d="M 71.7146 129.42 L 75.6026 129.42 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- U + + G - - C + + U - - C + + C - - U + + C - - U + + U - - U + + U - - A + + U - - U + + A - - U + + U - - C + + U - - C + + C - - C + + C - - A + + C - - G + + A - - C + + G - - C + + C - - A + + C - - A + + A - - 5' + d="M 74.4255 45.4847 A 1.78191,1.78191 270 0,0 72.6436,43.7028L 69.0798 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/T4_phage/tRNA-Gly-TCC.json b/inst/extdata/structures/T4_phage/tRNA-Gly-TCC.json index dbe689af..4201fd15 100644 --- a/inst/extdata/structures/T4_phage/tRNA-Gly-TCC.json +++ b/inst/extdata/structures/T4_phage/tRNA-Gly-TCC.json @@ -3,452 +3,452 @@ { "base": "G", "x": 69.55, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "C", "x": 69.76, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "G", "x": 69.55, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 69.55, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "A", "x": 69.97, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "U", "x": 69.76, - "y": 97.1, + "y": 89.54, "pos": 6 }, { 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xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.727" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Leu-TAA + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,299 +60,293 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 91.7766 117.916 L 94.5258 115.166 "/> + d="M 97.1223 123.261 L 99.8715 120.512 "/> + d="M 102.468 128.607 L 105.217 125.858 "/> + d="M 95.0847 107.803 L 95.0847 103.915 "/> + d="M 102.645 107.803 L 102.645 103.915 "/> + d="M 110.205 107.803 L 110.205 103.915 "/> + d="M 117.765 107.803 L 117.765 103.915 "/> - - - G - - - C + d="M 125.325 107.803 L 125.325 103.915 "/> + + G - - G + + C - - A + + G - - G + + A - - A + + G - - A + + A - - U + + A - - G + + U - - G + + G - - U + + G 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72.138 43.7028 "/> + + 5' diff --git a/inst/extdata/structures/T4_phage/tRNA-Pro-TGG.json b/inst/extdata/structures/T4_phage/tRNA-Pro-TGG.json index 8bacbbb7..a65d79ad 100644 --- a/inst/extdata/structures/T4_phage/tRNA-Pro-TGG.json +++ b/inst/extdata/structures/T4_phage/tRNA-Pro-TGG.json @@ -3,476 +3,476 @@ { "base": "C", "x": 74.57, - "y": 66.86, + "y": 59.3, "pos": 1 }, { "base": "U", "x": 74.57, - "y": 74.42, + "y": 66.86, "pos": 2 }, { "base": "C", "x": 74.57, - "y": 81.98, + "y": 74.42, "pos": 3 }, { "base": "C", "x": 74.57, - "y": 89.54, + "y": 81.98, "pos": 4 }, { "base": "G", "x": 74.36, - "y": 97.1, + "y": 89.54, "pos": 5 }, { "base": "U", "x": 74.57, - "y": 104.66, + "y": 97.1, "pos": 6 }, { "base": "G", "x": 74.36, - "y": 112.22, + "y": 104.66, "pos": 7 }, { "base": "U", "x": 67.14, - "y": 113.61, + "y": 106.05, "pos": 8 }, { "base": "A", "x": 61.17, - "y": 117.98, + "y": 110.42, "pos": 9 }, { "base": "G", "x": 56.97, - "y": 124.52, + "y": 116.96, "pos": 10 }, { "base": "C", 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"y": 104.66, + "y": 97.1, "pos": 68 }, { "base": "U", "x": 86.81, - "y": 97.1, + "y": 89.54, "pos": 69 }, { "base": "G", "x": 86.6, - "y": 89.54, + "y": 81.98, "pos": 70 }, { "base": "G", "x": 86.6, - "y": 81.98, + "y": 74.42, "pos": 71 }, { "base": "A", "x": 87.01, - "y": 74.42, + "y": 66.86, "pos": 72 }, { "base": "G", "x": 86.6, - "y": 66.86, + "y": 59.3, "pos": 73 }, { "base": "A", "x": 87.01, - "y": 59.3, + "y": 51.74, "pos": 74 }, { "base": "G", "x": 86.6, - "y": 51.74, + "y": 44.18, "pos": 75 }, { "base": "C", "x": 86.81, - "y": 44.18, + "y": 36.62, "pos": 76 }, { "base": "C", "x": 86.81, - "y": 36.62, + "y": 29.06, "pos": 77 }, { "base": "A", "x": 87.01, - "y": 29.06, + "y": 21.5, "pos": 78 } ], "width": 157.1, - "height": 206.96, + "height": 199.4, "lines": [], "trna_name": "tRNA-Pro-TGG", "sequence": "CUCCGUGUAGCUCAGUUUGGUAGAGCGCCUGAUUUGGGAUCAGGAGGUCCAAGGUUCAAAUCCUUGUAUGGAGAGCCA", "structure": "<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>....." -} +} \ No newline at end of file diff --git a/inst/extdata/structures/T4_phage/tRNA-Pro-TGG.svg b/inst/extdata/structures/T4_phage/tRNA-Pro-TGG.svg index ef45888c..33c7290f 100644 --- a/inst/extdata/structures/T4_phage/tRNA-Pro-TGG.svg +++ b/inst/extdata/structures/T4_phage/tRNA-Pro-TGG.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.101" - height="206.957" + height="199.397" id="svg2403" xml:space="preserve"> tRNA-Pro-TGG + @@ -30,19 +33,19 @@ d="M 81.4497 101.969 L 85.3377 101.969 "/> + d="M 59.8867 118.445 L 59.8867 122.333 "/> + d="M 52.3267 118.445 L 52.3267 122.333 "/> + d="M 44.7667 118.445 L 44.7667 122.333 "/> + d="M 37.2067 118.445 L 37.2067 122.333 "/> + d="M 74.5628 136.98 L 78.4508 136.98 "/> @@ -57,263 +60,257 @@ d="M 74.5628 167.22 L 78.4508 167.22 "/> + d="M 94.8747 115.363 L 94.8747 111.475 "/> + d="M 102.435 115.363 L 102.435 111.475 "/> + d="M 109.995 115.363 L 109.995 111.475 "/> + d="M 117.555 115.363 L 117.555 111.475 "/> - 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d="M 77.2737 53.0447 A 1.78191,1.78191 270 0,0 75.4918,51.2628L 71.928 51.2628 "/> + + 5' diff --git a/inst/extdata/structures/T4_phage/tRNA-Ser-TGA.json b/inst/extdata/structures/T4_phage/tRNA-Ser-TGA.json index 97fa2dc0..1dd40daf 100644 --- a/inst/extdata/structures/T4_phage/tRNA-Ser-TGA.json +++ b/inst/extdata/structures/T4_phage/tRNA-Ser-TGA.json @@ -3,548 +3,548 @@ { "base": "G", "x": 74.57, - "y": 59.3, + "y": 51.74, "pos": 1 }, { "base": "G", "x": 74.57, - "y": 66.86, + "y": 59.3, "pos": 2 }, { "base": "A", "x": 74.98, - "y": 74.42, + "y": 66.86, "pos": 3 }, { "base": "G", "x": 74.57, - "y": 81.98, + "y": 74.42, "pos": 4 }, { "base": "G", "x": 74.57, - "y": 89.54, + "y": 81.98, "pos": 5 }, { "base": "C", "x": 74.78, - "y": 97.1, + "y": 89.54, "pos": 6 }, { "base": "G", "x": 74.57, - "y": 104.66, + "y": 97.1, "pos": 7 }, { "base": "U", "x": 67.34, - "y": 106.05, + "y": 98.49, "pos": 8 }, { "base": "G", "x": 60.96, - "y": 110.42, + "y": 102.86, "pos": 9 }, { "base": "G", "x": 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a/inst/extdata/structures/T4_phage/tRNA-Ser-TGA.svg b/inst/extdata/structures/T4_phage/tRNA-Ser-TGA.svg index 3772bba7..d8f013b2 100644 --- a/inst/extdata/structures/T4_phage/tRNA-Ser-TGA.svg +++ b/inst/extdata/structures/T4_phage/tRNA-Ser-TGA.svg @@ -4,12 +4,15 @@ xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" width="157.311" - height="199.397" + height="191.837" id="svg2403" xml:space="preserve"> tRNA-Ser-TGA + @@ -30,19 +33,19 @@ d="M 81.6597 94.4085 L 85.5477 94.4085 "/> + d="M 60.0967 110.885 L 60.0967 114.773 "/> + d="M 52.5367 110.885 L 52.5367 114.773 "/> + d="M 44.9767 110.885 L 44.9767 114.773 "/> + d="M 37.4167 110.885 L 37.4167 114.773 "/> + d="M 74.7728 129.42 L 78.6608 129.42 "/> @@ -57,317 +60,311 @@ d="M 74.7728 159.66 L 78.6608 159.66 "/> + d="M 91.7766 117.916 L 94.5258 115.166 "/> + d="M 97.1223 123.261 L 99.8715 120.512 "/> + d="M 102.468 128.607 L 105.217 125.858 "/> + d="M 107.814 133.953 L 110.563 131.204 "/> + d="M 113.159 139.299 L 115.909 136.549 "/> 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