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EMBOSS: antigenic |
Analysis of data from experimentally determined antigenic sites on proteins has revealed that the hydrophobic residues Cys, Leu and Val, if they occur on the surface of a protein, are more likely to be a part of antigenic sites. A semi-empirical method which makes use of physicochemical properties of amino acid residues and their frequencies of occurrence in experimentally known segmental epitopes was developed by Kolaskar and Tongaonkar to predict antigenic determinants on proteins. Application of this method to a large number of proteins has shown that their method can predict antigenic determinants with about 75% accuracy which is better than most of the known methods. This method is based on a single parameter and thus very simple to use.
% antigenic Finds antigenic sites in proteins Input sequence: sw:act1_fugru Minimum length [6]: Output file [act1_fugru.antigenic]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA -minlen integer Minimum length [-outfile] report (no help text) report value Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-minlen | Minimum length | Integer from 1 to 50 | 6 |
[-outfile] (Parameter 2) |
(no help text) report value | Report file | |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
The output is a standard EMBOSS report file.
The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq
See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.
By default antigenic writes a 'motif' report file.
The output from the above example is:
######################################## # Program: antigenic # Rundate: Mon Feb 11 12:01:10 2002 # Report_file: act1_fugru.antigenic ######################################## #======================================= # # Sequence: ACT1_FUGRU from: 1 to: 375 # HitCount: 18 #======================================= Max_score_pos at "*" (1) Score 1.207 length 9 at residues 214->222 * Sequence: EKLCYVALD | | 214 222 (2) Score 1.187 length 15 at residues 131->145 * Sequence: AMYVAIQAVLSLYAS | | 131 145 (3) Score 1.166 length 8 at residues 5->12 * Sequence: IAALVVDN | | 5 12 (4) Score 1.164 length 12 at residues 27->38 * Sequence: PRAVFPSIVGRP | | 27 38 (5) Score 1.136 length 24 at residues 160->183 * Sequence: THTVPIYEGYALPHAILRLDLAGR | | 160 183 (6) Score 1.135 length 6 at residues 367->372 * Sequence: PSIVHR | | 367 372 (7) Score 1.116 length 16 at residues 93->108 * Sequence: ELRVAPEEHPVLLTEA | | 93 108 (8) Score 1.113 length 7 at residues 295->301 * Sequence: ANTVLSG | | 295 301 (9) Score 1.110 length 11 at residues 256->266 * Sequence: RCPEALFQPSF | | 256 266 (10) Score 1.107 length 17 at residues 336->352 * Sequence: KYSVWIGGSILASLSTF | | 336 352 (11) Score 1.102 length 15 at residues 62->76 * Sequence: RGILTLKYPIEHGIV | | 62 76 (12) Score 1.086 length 19 at residues 232->250 * Sequence: SSSSLEKSYELPDGQVITI | | 232 250 (13) Score 1.083 length 6 at residues 327->332 * Sequence: IKIIAP | | 327 332 (14) Score 1.074 length 7 at residues 317->323 * Sequence: ITALAPS | | 317 323 (15) Score 1.068 length 7 at residues 186->192 * Sequence: TDYLMKI | | 186 192 (16) Score 1.066 length 7 at residues 40->46 * Sequence: HQGVMVG | | 40 46 (17) Score 1.045 length 7 at residues 269->275 * Sequence: MESCGIH | | 269 275 (18) Score 1.034 length 7 at residues 51->57 * Sequence: DSYVGDE | | 51 57 #--------------------------------------- #---------------------------------------
% antigenic -rformat gff Finds antigenic sites in proteins Input sequence(s): sw:act1_fugru Minimum length [6]: Output file [act1_fugru.antigenic]: % more act1_fugru.antigenic ##gff-version 2.0 ##date 2002-02-11 ##Type Protein ACT1_FUGRU ACT1_FUGRU antigenic site 214 222 1.207 + . Sequence "ACT1_FUGRU.1" ; note "*pos 218" ACT1_FUGRU antigenic site 131 145 1.187 + . Sequence "ACT1_FUGRU.2" ; note "*pos 137" ACT1_FUGRU antigenic site 5 12 1.166 + . Sequence "ACT1_FUGRU.3" ; note "*pos 8" ACT1_FUGRU antigenic site 27 38 1.164 + . Sequence "ACT1_FUGRU.4" ; note "*pos 32" ACT1_FUGRU antigenic site 160 183 1.136 + . Sequence "ACT1_FUGRU.5" ; note "*pos 173" ACT1_FUGRU antigenic site 367 372 1.135 + . Sequence "ACT1_FUGRU.6" ; note "*pos 372" ACT1_FUGRU antigenic site 93 108 1.116 + . Sequence "ACT1_FUGRU.7" ; note "*pos 103" ACT1_FUGRU antigenic site 295 301 1.113 + . Sequence "ACT1_FUGRU.8" ; note "*pos 296" ACT1_FUGRU antigenic site 256 266 1.110 + . Sequence "ACT1_FUGRU.9" ; note "*pos 264" ACT1_FUGRU antigenic site 336 352 1.107 + . Sequence "ACT1_FUGRU.10" ; note "*pos 347" ACT1_FUGRU antigenic site 62 76 1.102 + . Sequence "ACT1_FUGRU.11" ; note "*pos 68" ACT1_FUGRU antigenic site 232 250 1.086 + . Sequence "ACT1_FUGRU.12" ; note "*pos 245" ACT1_FUGRU antigenic site 327 332 1.083 + . Sequence "ACT1_FUGRU.13" ; note "*pos 330" ACT1_FUGRU antigenic site 317 323 1.074 + . Sequence "ACT1_FUGRU.14" ; note "*pos 320" ACT1_FUGRU antigenic site 186 192 1.068 + . Sequence "ACT1_FUGRU.15" ; note "*pos 191" ACT1_FUGRU antigenic site 40 46 1.066 + . Sequence "ACT1_FUGRU.16" ; note "*pos 43" ACT1_FUGRU antigenic site 269 275 1.045 + . Sequence "ACT1_FUGRU.17" ; note "*pos 269" ACT1_FUGRU antigenic site 51 57 1.034 + . Sequence "ACT1_FUGRU.18" ; note "*pos 52"
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by EMBOSS environment variable EMBOSS_DATA.
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
Here is the default Eantigenic.dat file:
# Antigenic Surface Antigenic # Amino -- Occurrence of amino acids in -- frequency frequency propensity # Acid Epitopes Surface Protein f(Ag) f(s) A(p) A 135 328 524 0.065 0.061 1.064 C 53 97 186 0.026 0.018 1.412 D 118 352 414 0.057 0.066 0.866 E 132 401 499 0.064 0.075 0.851 F 76 180 365 0.037 0.034 1.091 G 116 343 487 0.056 0.064 0.874 H 59 138 191 0.029 0.026 1.105 I 86 193 437 0.042 0.036 1.152 K 158 439 523 0.076 0.082 0.930 L 149 308 684 0.072 0.058 1.250 M 23 72 152 0.011 0.013 0.826 N 94 313 407 0.045 0.058 0.776 P 135 328 411 0.065 0.061 1.064 Q 99 252 332 0.048 0.047 1.015 R 106 314 394 0.051 0.058 0.873 S 168 429 553 0.081 0.080 1.012 T 141 401 522 0.068 0.075 0.909 V 128 239 515 0.062 0.045 1.383 W 19 55 103 0.009 0.010 0.893 Y 71 158 245 0.034 0.029 1.161 Total 2066 5340 7944
Program name | Description |
---|---|
digest | Protein proteolytic enzyme or reagent cleavage digest |
fuzzpro | Protein pattern search |
fuzztran | Protein pattern search after translation |
helixturnhelix | Report nucleic acid binding motifs |
oddcomp | Finds protein sequence regions with a biased composition |
patmatdb | Search a protein sequence with a motif |
patmatmotifs | Search a PROSITE motif database with a protein sequence |
pepcoil | Predicts coiled coil regions |
preg | Regular expression search of a protein sequence |
pscan | Scans proteins using PRINTS |
sigcleave | Reports protein signal cleavage sites |
Original program "ANTIGENIC" by Peter Rice (EGCG 1991)