EMBOSS: antigenic

Program antigenic

Function

Description

Usage

% 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

Output file format

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

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:

• . (your current directory)
• .embossdata (under your current directory)
• ~/ (your home directory)
• ~/.embossdata

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

Diagnostic Error Messages

Exit status

Known bugs

Author(s)

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

History

Target users

Comments