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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) |
ANTIGENIC of ACT1_FUGRU from: 1 to: 375 Length 375 residues, score calc from 4 to 372 Reporting all peptides over 6 residues Found 18 hits scoring over 1.00 (true average 1.02) Maximum length 24 at residues 160->183 Sequence: THTVPIYEGYALPHAILRLDLAGR | | 160 183 Entries in score order, max score 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
% antigenic -featout eg.gff Finds antigenic sites in proteins Input sequence(s): sw:act1_fugru Minimum length [6]: Output file [act1_fugru.antigenic]: % more eg.gff ##gff-version 0.0 ##date 2001-02-13 ##sequence-region ACT1_FUGRU 0 0 ACT1_FUGRU antigenic misc_feature 5 12 1.166 + . note "max score at 7" ACT1_FUGRU antigenic misc_feature 27 38 1.164 + . note "max score at 31" ACT1_FUGRU antigenic misc_feature 40 46 1.066 + . note "max score at 42" ACT1_FUGRU antigenic misc_feature 51 57 1.034 + . note "max score at 51" ACT1_FUGRU antigenic misc_feature 62 76 1.102 + . note "max score at 67" ACT1_FUGRU antigenic misc_feature 93 108 1.116 + . note "max score at 102 ,103" ACT1_FUGRU antigenic misc_feature 131 145 1.187 + . note "max score at 136" ACT1_FUGRU antigenic misc_feature 160 183 1.136 + . note "max score at 172" ACT1_FUGRU antigenic misc_feature 186 192 1.068 + . note "max score at 190" ACT1_FUGRU antigenic misc_feature 214 222 1.207 + . note "max score at 217" ACT1_FUGRU antigenic misc_feature 232 250 1.086 + . note "max score at 244" ACT1_FUGRU antigenic misc_feature 256 266 1.110 + . note "max score at 263" ACT1_FUGRU antigenic misc_feature 269 275 1.045 + . note "max score at 268" ACT1_FUGRU antigenic misc_feature 295 301 1.113 + . note "max score at 295" ACT1_FUGRU antigenic misc_feature 317 323 1.074 + . note "max score at 319" ACT1_FUGRU antigenic misc_feature 327 332 1.083 + . note "max score at 329" ACT1_FUGRU antigenic misc_feature 336 352 1.107 + . note "max score at 346" ACT1_FUGRU antigenic misc_feature 367 372 1.135 + . note "max score at 371"
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)