EMBOSS: antigenic


Program antigenic

Function

Finds antigenic sites in proteins

Description

Antigenic predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.

Usage

Here is a sample session with antigenic.

% antigenic
Finds antigenic sites in proteins
Input sequence: sw:act1_fugru
Minimum length [6]: 
Output file [act1_fugru.antigenic]: 

Command line arguments

   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

Input file format

The input sequence can be one or more protein sequences.

Output file format

Here is a sample output:

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


Data files

Antigenic uses a data file called Eantigenic.dat.

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

Notes

References

  1. Kolaskar,AS and Tongaonkar,PC (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Letters 276: 172-174.
  2. Parker,JMR, Guo,D and Hodges,RS (1986). Biochemistry 25: 5425-5432.

Warnings

The program will warn you if the sequence is not a protein or has ambiguity codes.

Diagnostic Error Messages

Exit status

It exits with status 0, unless a region is badly constructed.

Known bugs

None.

See also

Program nameDescription
diffseqFind differences (SNPs) between nearly identical sequences
dotmatcherDisplays a thresholded dotplot of two sequences
dotpathDisplays a non-overlapping wordmatch dotplot of two sequences
dottupDisplays a wordmatch dotplot of two sequences
garnierPredicts protein secondary structure
helixturnhelixReport nucleic acid binding motifs
oddcompFinds protein sequence regions with a biased composition
pepcoilPredicts coiled coil regions
polydotDisplays all-against-all dotplots of a set of sequences
pscanScans proteins using PRINTS
showseqDisplay a sequence with features, translation etc
sigcleaveReports protein signal cleavage sites
tmapDisplays membrane spanning regions

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

Original program "ANTIGENIC" by Peter Rice (EGCG 1991)

History

Completed 9th March 1999

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments