Add missing special tRNA structures (fMet, Ile2, SeC)#26
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jayhesselberth wants to merge 1 commit intodevelfrom
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Add missing special tRNA structures (fMet, Ile2, SeC)#26jayhesselberth wants to merge 1 commit intodevelfrom
jayhesselberth wants to merge 1 commit intodevelfrom
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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) <noreply@anthropic.com>
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Summary
generate_svgs.pythat silently excluded fMet, Ile2, and SeC tRNAs (GtRNAdb usesfMet/Ile2/SeCbut MODOMICS usesIni/Ile/Sec)TRNAinf-*-SeC.cm) for correct structural alignment of the 95 nt selenocysteine tRNATest plan
devtools::test()passes (479/479)plot_tRNA_structure()🤖 Generated with Claude Code