Computational structural immunology tool for analyzing immune interfaces
Usage: /data/apps/vdjdock/bin/epimorph.pl
Standard options
--epitopedb=epitopes.txt database of epitopes, with each line containing
space separated list of positions that make up
the epitope.
example: A:119 A:122 A:124 A:125 A:127 A:133 A:146 A:149 A:152 A:67
B:125 B:147 B:150 B:151 B:160 B:161 C:4 C:5 D:11 D:9
B:14 B:150 B:20 B:25 B:28 B:30 B:31 B:32 B:33 B:34
--alignment=MSA.fa a set of sequences aligned to the structural
reference antigen. It is an MSA with every residue of
the reference structure present and no gaps relative to
the reference structure, such that MSA length = ref sequence length
example: >structure
EDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAG
>H1N1-2009
EDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAG
--numbering=number.txt a mapping file assigning a structural number ID
to each position in the sequence of the structural
reference found in the MSA.fa. Format is three tabs
separated seqposition|AA|structuralnumber
example: Residue_Number Residue_AA Structure_Number
0 E A:4
1 D A:5
2 Q A:6
3 I A:7
--antigen=[state] one of the sequence names as the antigen. then for each epitope
code will report all MSA variants that share that epitope with
antigen
--sanity_check=1 [OPTIONAL] if antigen is set to reference structure sequence, it makes sure that
the numbering in numbering.txt always matches the alignment or returns
an error message. Note --antigen needs to be the structural ref for this!
--centivax_min_conc=1 [OPTIONAL] minimum number of centivax members to share an epitope here for this epitope
to count as above threshold dose. If set to 3, then at least one epitope must be shared
between three members of centivax for this site to be counted as present in the mixture
--forbidden_contact_list a file that contains forbidden structIDs, one per line. For disallowing certain epitopes
(stem binding, etc)
Reference set of human antibody docking templates: 559 antibodies:
1ADQ,1AQK,1BEY,1DFB,1DN0,1DQL,1FGV,1G9M,1HZH,1IGA,1IGM,1IQD,1L7I,1NFD,1NL0,1Q1J,1RHH,1RZ7,1RZF,1RZG,1RZI,1T4K,1TJG,1TZI,1U6A,1W72,2A9N,2AGJ,2AJ3,2B0S,2B2X,2CMR,2D7T,2EIZ,2FGW,2FJH,2FL5,2H9G,2HFF,2HWZ,2J6E,2QQN,2QSC,2R0L,2R56,2UZI,2VXQ,2VXV,2X7L,2XA8,2XQB,2XRA,2XWT,2XZA,2YBR,3AAZ,3BQU,3EO0,3EO9,3EYF,3F12,3FN0,3FZU,3G04,3G6A,3G6J,3GBM,3GHE,3GO1,3H0T,3H42,3HC0,3HI5,3HMW,3IDX,3IYW,3J5M,3J6U,3JCB,3K2U,3KR3,3KYK,3L95,3LMJ,3LRS,3LZF,3M8O,3MLR,3MLW,3MLX,3N85,3NAC,3NGB,3NH7,3P0V,3P30,3PIQ,3Q6G,3QEG,3QEH,3QPX,3SDY,3SE8,3SKJ,3SQO,3T2N,3TCL,3THM,3TNM,3TNN,3TV3,3TWC,3U0T,3U1S,3U30,3U6R,3U7W,3UAJ,3UJI,3UJJ,3ULS,3W9D,3WD5,3WHE,3WLW,3WSQ,3X3F,4C2I,4CNI,4D9L,4D9Q,4DAG,4DGV,4DKF,4EDW,4EOW,4ERS,4F57,4FNL,4FQ1,4FQ2,4FQH,4FQJ,4FQL,4FQQ,4FZ8,4FZE,4G5Z,4G6F,4GLR,4GSD,4GW4,4GXU,4HBC,4HCR,4HF5,4HFU,4HFW,4HG4,4HH9,4HIE,4HIX,4HS6,4HS8,4HT1,4I77,4IDJ,4J4P,4J6R,4JAM,4JB9,4JFZ,4JHA,4JM2,4JO1,4JO3,4JPV,4JPW,4JY6,4K3J,4KRP,4KTD,4KTE,4KVN,4KY1,4LEO,4LMQ,4LRI,4LSP,4LSU,4M5Y,4M6O,4MA3,4MWF,4MXV,4N0Y,4N90,4N9G,4NHH,4NKI,4NM4,4NP4,4NPY,4NRX,4NUJ,4NZU,4O58,4O9H,4OAW,4OCS,4OCW,4OD1,4OD2,4OD3,4OLX,4OQT,4OSU,4PS4,4PTT,4PY7,4Q2Z,4QHL,4R26,4R4B,4R7D,4R8W,4R90,4RAV,4RFE,4RFO,4RX4,4RZC,4S1Q,4S1R,4S1S,4TSA,4U6V,4UAO,4UIF,4UOK,4UT6,4UT7,4UTA,4UU9,4UV4,4V1D,4WUU,4WV1,4XHJ,4XI5,4XMK,4XMP,4XNY,4XNZ,4XVJ,4XVS,4XXD,4Y5V,4Y5Y,4YAQ,4YDI,4YDJ,4YDK,4YDL,4YDV,4YE4,4YFL,4YHZ,4YPG,4YWG,4Z0X,4Z5R,4ZS6,4ZS7,4ZTO,4ZYK,5A3I,5ALB,5ANM,5AWN,5B71,5BK0,5BK3,5BMF,5BQ7,5BZD,5BZW,5C0N,5C6T,5C7X,5CCK,5CD3,5CEX,5CEZ,5CGY,5CHN,5CIL,5CJX,5CZV,5CZX,5D1Q,5D1X,5D1Z,5D6C,5DD6,5DMG,5DR5,5DRW,5DRX,5DRZ,5DSC,5DTF,5DUM,5DUR,5DWU,5E8E,5EA0,5ESV,5EWI,5F6H,5F6I,5F89,5F96,5F9O,5F9W,5FEH,5FGC,5FHA,5FHB,5FUO,5GGQ,5GGT,5GJS,5GMQ,5GS0,5I1E,5I5K,5I8C,5I8K,5I8O,5I9Q,5IBT,5IBU,5IIE,5IJK,5ITB,5JO4,5JO5,5JRP,5JZ7,5K9J,5K9Q,5KAN,5KAQ,5KEM,5KVL,5KW9,5L6Y,5LSP,5N4G,5N4J,5N7W,5NGV,5NYX,5O14,5O4G,5OB5,5OCK,5OTJ,5SX4,5T33,5T3X,5TE4,5TLK,5TPL,5TPN,5TPP,5TQA,5TRP,5TY6,5TZT,5U3J,5U3K,5U3M,5U3P,5U4R,5UBZ,5UD9,5UEK,5UEL,5UEM,5UG0,5UIX,5UKO,5UMI,5USL,5UXQ,5V2A,5V6L,5V6M,5V7R,5V7U,5VAG,5VIC,5VIG,5VK2,5VL7,5VOB,5VOD,5VQM,5W08,5W1G,5W1K,5W42,5W6G,5WB9,5WCA,5WCC,5WCD,5WDF,5WHJ,5WKO,5WNA,5WUV,5X8L,5X8M,5XAJ,5XHV,5XMH,5XWD,5Y2K,5Y9J,5YOY,5YY5,5ZIA,5ZV3,6A4K,6A67,6AL4,6APB,6AVN,6AXK,6AXL,6B08,6B0A,6B0E,6B0G,6B0H,6B3M,6B5L,6B9J,6BA5,6BCK,6BE2,6BF4,6BFQ,6BGT,6BKB,6BKC,6BKD,6BLA,6BLI,6BP2,6BQB,6BTJ,6C6X,6C9U,6CA6,6CA7,6CJK,6CMG,6CNR,6CT7,6CWT,6CYF,6D11,6D2P,6DB5,6DB6,6DB7,6DC3,6DCV,6DEZ,6DF0,6DFI,6DL8,6DLB,6DW2,6DWI,6E3H,6E4X,6E56,6E62,6E63,6EAY,6FG1,6FGB,6FOE,6FY0,6FY3,6GFE,6GG0,6GKU,6GLW,6GLX,6HIG,6HJP,6I04,6I9I,6IAP,6IEC,6IEK,6II4,6II9,6IUT,6IUV,6IVZ,6JEP,6K7O,6MED,6MEE,6MEG,6MHR,6MID,6MJZ,6MNQ,6MNR,6MQC,6MQE,6MQR,6MQS,6MTO,6MTP,6MTQ,6MTR,6MTS,6MTT,6N16,6N7J,6N81,6N8D,6NB3,6NB6,6NC2,6NN3,6NOV,6NZ7,6O39,6OBZ,6OE4,6OGX,6OL5,6OL7,6ORO,6ORP,6RCQ,6RCS,7FAB,8FAB
Examples:
#H3N2-1997
for file in split-*txt # *top.top.txt *bot.top.txt *bot.tail.txt *top.tail.txt
do
bsub "../bin/epimorph-conservation.pl --epitopedb=$file --alignment=alignment-publication-curated.msa.fa --numbering=numbering.txt --antigen=$target > ${target}-${file}-conservation"
#bsub "../bin/epimorph.pl --epitopedb=$file --alignment=alignment-publication-curated.msa.fa --numbering=numbering.txt --antigen=$target > ${target}-${file}"
done
target="H1N1" #-2007"
#H3N2-1997
for depth in 11 # 2 3 4 5 6 7
do
for file in split-*txt # *top.top.txt *bot.top.txt *bot.tail.txt *top.tail.txt
do
bsub "../bin/epimorph.pl --epitopedb=$file --alignment=alignment-publication-curated.msa.fa --numbering=numbering.txt --antigen=$target --centivax_min_conc=$depth > centivax-${target}-${file}-${depth}.txt"
done
done
target="H1N1-2007"
#H3N2-1997
for file in split-*txt # *top.top.txt *bot.top.txt *bot.tail.txt *top.tail.txt
do
bsub "../bin/epimorph.pl --epitopedb=$file --alignment=alignment-publication-curated.msa.fa --numbering=numbering.txt --antigen=$target > ${target}-${file}"
done
target="H3N2" #-2007"
#H3N2-1997
for depth in 2 3 4 5 6 7 # 8 9 10 #11 # 2 3 4 5 6 7
do
for file in split-*txt # *top.top.txt *bot.top.txt *bot.tail.txt *top.tail.txt
do
bsub "../bin/epimorph.pl --epitopedb=$file --alignment=alignment-publication-curated.msa.fa --numbering=numbering.txt --antigen=$target --centivax_min_conc=$depth > centivax-${target}-${file}-${depth}.txt"
done
done
#../bin/epimorph.pl --epitopedb=10k.sample.txt --alignment=alignment-publication-curated.msa.fa --numbering=numbering.txt --antigen=H1N1 --centivax_min_conc=2