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EMBOSS: antigenic |
% 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] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -featout featout File for output features |
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) |
Output file name | Output file | <sequence>.antigenic |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-featout | File for output features | Writeable feature table | unknown.gff |
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
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 |
---|---|
diffseq | Find differences (SNPs) between nearly identical sequences |
dotmatcher | Displays a thresholded dotplot of two sequences |
dotpath | Displays a non-overlapping wordmatch dotplot of two sequences |
dottup | Displays a wordmatch dotplot of two sequences |
garnier | Predicts protein secondary structure |
helixturnhelix | Report nucleic acid binding motifs |
oddcomp | Finds protein sequence regions with a biased composition |
pepcoil | Predicts coiled coil regions |
polydot | Displays all-against-all dotplots of a set of sequences |
pscan | Scans proteins using PRINTS |
showseq | Display a sequence with features, translation etc |
sigcleave | Reports protein signal cleavage sites |
tmap | Displays membrane spanning regions |
Original program "ANTIGENIC" by Peter Rice (EGCG 1991)