EMBOSS: antigenic

| antigenic

## Function

Finds antigenic sites in proteins

## Description

Antigenic predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. This method is based on a single parameter and thus very simple to use.

## Algorithm

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. The method of Kolaskar and Tongaonkar to predict antigenic determinants in proteins is semi-empirical and makes use of physicochemical properties of amino acid residues and their frequencies of occurrence in experimentally known segmental epitopes.

## Usage

Here is a sample session with antigenic

    % antigenic
    Finds antigenic sites in proteins
    Input protein sequence(s): tsw:actb1_fugru
    Minimum length of antigenic region [6]:
    Output report [actb1_fugru.antigenic]:

Go to the input files for this example
Go to the output files for this example

Example 2

By using the '-rformat gff' qualifier, a GFF file of the predicted regions can be produced.

    % antigenic -rformat gff
    Finds antigenic sites in proteins
    Input protein sequence(s): tsw:actb1_fugru
    Minimum length of antigenic region [6]:
    Output report [actb1_fugru.antigenic]:

Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     Protein sequence(s) filename and optional
                                      format, or reference (input USA)
       -minlen             integer    [6] Minimum length of antigenic region
                                      (Integer from 1 to 50)
      [-outfile]           report     [*.antigenic] Output report file name

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of each sequence to be used
       -send1              integer    End of each sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-outfile" associated qualifiers
       -rformat2           string     Report format
       -rname2             string     Base file name
       -rextension2        string     File name extension
       -rdirectory2        string     Output directory
       -raccshow2          boolean    Show accession number in the report
       -rdesshow2          boolean    Show description in the report
       -rscoreshow2        boolean    Show the score in the report
       -rstrandshow2       boolean    Show the nucleotide strand in the report
       -rusashow2          boolean    Show the full USA in the report
       -rmaxall2           integer    Maximum total hits to report
       -rmaxseq2           integer    Maximum hits to report for one sequence

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
-minlen | Minimum length of antigenic region | Integer from 1 to 50 | 6
[-outfile] (Parameter 2) | Output report file name | Report output file | <*>.antigenic
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

The input sequence can be one or more protein sequences.

### Input files for usage example

'tsw:actb1_fugru' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:actb1_fugru

    ID   ACTB1_FUGRU             Reviewed;         375 AA.
    AC   P68142; P53484;
    DT   25-OCT-2004, integrated into UniProtKB/Swiss-Prot.
    DT   25-OCT-2004, sequence version 1.
    DT   20-MAR-2007, entry version 16.
    DE   Actin, cytoplasmic 1 (Beta-actin A).
    GN   Name=ACTB-A;
    OS   Fugu rubripes (Japanese pufferfish) (Takifugu rubripes).
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
    OC   Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei;
    OC   Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes;
    OC   Tetradontoidea; Tetraodontidae; Takifugu.
    OX   NCBI_TaxID=31033;
    RN   [1]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND TISSUE SPECIFICITY.
    RX   MEDLINE=96275651; PubMed=8683572; DOI=10.1006/jmbi.1996.0347;
    RA   Venkatesh B., Tay B.H., Elgar G., Brenner S.;
    RT   "Isolation, characterization and evolution of nine pufferfish (Fugu
    RT   rubripes) actin genes.";
    RL   J. Mol. Biol. 259:655-665(1996).
    CC   -!- FUNCTION: Actins are highly conserved proteins that are involved
    CC       in various types of cell motility and are ubiquitously expressed
    CC       in all eukaryotic cells.
    CC   -!- SUBUNIT: Polymerization of globular actin (G-actin) leads to a
    CC       structural filament (F-actin) in the form of a two-stranded helix.
    CC       Each actin can bind to 4 others.
    CC   -!- SUBCELLULAR LOCATION: Cytoplasm.
    CC   -!- TISSUE SPECIFICITY: Widely distributed. Not expressed in skeletal
    CC       muscle.
    CC   -!- MISCELLANEOUS: In vertebrates 3 main groups of actin isoforms,
    CC       alpha, beta and gamma have been identified. The alpha actins are
    CC       found in muscle tissues and are a major constituent of the
    CC       contractile apparatus. The beta and gamma actins coexist in most
    CC       cell types as components of the cytoskeleton and as mediators of
    CC       internal cell motility.
    CC   -!- MISCELLANEOUS: There are three different beta-cytoplasmic actins
    CC       in Fugu rubripes.
    CC   -!- SIMILARITY: Belongs to the actin family.
    CC   -----------------------------------------------------------------------
    CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
    CC   Distributed under the Creative Commons Attribution-NoDerivs License
    CC   -----------------------------------------------------------------------
    DR   EMBL; U37499; AAC59889.1; -; Genomic_DNA.
    DR   PIR; S71124; S71124.
    DR   HSSP; P02570; 1HLU.
    DR   SMR; P68142; 4-371.
    DR   Ensembl; NEWSINFRUG00000152503; Fugu rubripes.
    DR   InterPro; IPR004001; Actin.
    DR   InterPro; IPR004000; Actin_like.
    DR   PANTHER; PTHR11937; Actin_like; 1.
    DR   Pfam; PF00022; Actin; 1.
    DR   PRINTS; PR00190; ACTIN.
    DR   SMART; SM00268; ACTIN; 1.
    DR   PROSITE; PS00406; ACTINS_1; 1.
    DR   PROSITE; PS00432; ACTINS_2; 1.
    DR   PROSITE; PS01132; ACTINS_ACT_LIKE; 1.
    KW   Acetylation; ATP-binding; Cytoskeleton; Methylation;
    KW   Nucleotide-binding; Structural protein.
    FT   PROPEP        1      1       Removed in mature form (By similarity).
    FT                                /FTId=PRO_0000000808.
    FT   CHAIN         2    375       Actin, cytoplasmic 1.
    FT                                /FTId=PRO_0000000809.
    FT   MOD_RES       1      1       N-acetylmethionine (By similarity).
    FT   MOD_RES       2      2       N-acetylglutamate (By similarity).
    FT   MOD_RES      73     73       Tele-methylhistidine (By similarity).
    SQ   SEQUENCE   375 AA;  41767 MW;  9C505616D33E9495 CRC64;
         MEDEIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS
         KRGILTLKYP IEHGIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT
         QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT HTVPIYEGYA LPHAILRLDL
         AGRDLTDYLM KILTERGYSF TTTAEREIVR DIKEKLCYVA LDFEQEMGTA ASSSSLEKSY
         ELPDGQVITI GNERFRCPEA LFQPSFLGME SCGIHETTYN SIMKCDVDIR KDLYANTVLS
         GGTTMYPGIA DRMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWISKQ
         EYDESGPSIV HRKCF
    //

## Output file format

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://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.

By default antigenic writes a 'motif' report file.

### Output files for usage example

### File: actb1_fugru.antigenic

    ########################################
    # Program: antigenic
    # Rundate: Tue 15 Jul 2008 12:00:00
    # Commandline: antigenic
    #    -sequence tsw:actb1_fugru
    # Report_format: motif
    # Report_file: actb1_fugru.antigenic
    ########################################

    #=======================================
    #
    # Sequence: ACTB1_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
     Max_score_pos: 218

    (2) Score 1.187 length 15 at residues 131->145
                     *
     Sequence: AMYVAIQAVLSLYAS
               |             |
             131             145
     Max_score_pos: 137

    (3) Score 1.166 length 8 at residues 5->12
                  *
     Sequence: IAALVVDN
               |      |
               5      12
     Max_score_pos: 8

    (4) Score 1.164 length 12 at residues 27->38
                    *
     Sequence: PRAVFPSIVGRP
               |          |
              27          38
     Max_score_pos: 32

    (5) Score 1.136 length 24 at residues 160->183
                            *
     Sequence: THTVPIYEGYALPHAILRLDLAGR
               |                      |
             160                      183

      [Part of this file has been deleted for brevity]

                            *
     Sequence: SSSSLEKSYELPDGQVITI
               |                 |
             232                 250
     Max_score_pos: 245

    (13) Score 1.083 length 6 at residues 327->332
                  *
     Sequence: IKIIAP
               |    |
             327    332
     Max_score_pos: 330

    (14) Score 1.074 length 7 at residues 317->323
                  *
     Sequence: ITALAPS
               |     |
             317     323
     Max_score_pos: 320

    (15) Score 1.068 length 7 at residues 186->192
                    *
     Sequence: TDYLMKI
               |     |
             186     192
     Max_score_pos: 191

    (16) Score 1.066 length 7 at residues 40->46
                  *
     Sequence: HQGVMVG
               |     |
              40     46
     Max_score_pos: 43

    (17) Score 1.045 length 7 at residues 269->275
               *
     Sequence: MESCGIH
               |     |
             269     275
     Max_score_pos: 269

    (18) Score 1.034 length 7 at residues 51->57
                *
     Sequence: DSYVGDE
               |     |
              51     57
     Max_score_pos: 52

    #---------------------------------------
    #---------------------------------------

### Output files for usage example 2

### File: actb1_fugru.antigenic

    ##gff-version 2.0
    ##date 2007-07-15
    ##Type Protein ACTB1_FUGRU
    ACTB1_FUGRU	antigenic	region	214	222	1.207	+	.	Sequence "ACTB1_FUGRU.1" ; note "*pos 218"
    ACTB1_FUGRU	antigenic	region	131	145	1.187	+	.	Sequence "ACTB1_FUGRU.2" ; note "*pos 137"
    ACTB1_FUGRU	antigenic	region	5	12	1.166	+	.	Sequence "ACTB1_FUGRU.3" ; note "*pos 8"
    ACTB1_FUGRU	antigenic	region	27	38	1.164	+	.	Sequence "ACTB1_FUGRU.4" ; note "*pos 32"
    ACTB1_FUGRU	antigenic	region	160	183	1.136	+	.	Sequence "ACTB1_FUGRU.5" ; note "*pos 173"
    ACTB1_FUGRU	antigenic	region	367	372	1.135	+	.	Sequence "ACTB1_FUGRU.6" ; note "*pos 372"
    ACTB1_FUGRU	antigenic	region	93	108	1.116	+	.	Sequence "ACTB1_FUGRU.7" ; note "*pos 103"
    ACTB1_FUGRU	antigenic	region	295	301	1.113	+	.	Sequence "ACTB1_FUGRU.8" ; note "*pos 296"
    ACTB1_FUGRU	antigenic	region	256	266	1.110	+	.	Sequence "ACTB1_FUGRU.9" ; note "*pos 264"
    ACTB1_FUGRU	antigenic	region	336	352	1.107	+	.	Sequence "ACTB1_FUGRU.10" ; note "*pos 347"
    ACTB1_FUGRU	antigenic	region	62	76	1.102	+	.	Sequence "ACTB1_FUGRU.11" ; note "*pos 68"
    ACTB1_FUGRU	antigenic	region	232	250	1.086	+	.	Sequence "ACTB1_FUGRU.12" ; note "*pos 245"
    ACTB1_FUGRU	antigenic	region	327	332	1.083	+	.	Sequence "ACTB1_FUGRU.13" ; note "*pos 330"
    ACTB1_FUGRU	antigenic	region	317	323	1.074	+	.	Sequence "ACTB1_FUGRU.14" ; note "*pos 320"
    ACTB1_FUGRU	antigenic	region	186	192	1.068	+	.	Sequence "ACTB1_FUGRU.15" ; note "*pos 191"
    ACTB1_FUGRU	antigenic	region	40	46	1.066	+	.	Sequence "ACTB1_FUGRU.16" ; note "*pos 43"
    ACTB1_FUGRU	antigenic	region	269	275	1.045	+	.	Sequence "ACTB1_FUGRU.17" ; note "*pos 269"
    ACTB1_FUGRU	antigenic	region	51	57	1.034	+	.	Sequence "ACTB1_FUGRU.18" ; note "*pos 52"

## 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 the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

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

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.

## 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 name | Description
--- | ---
digest | Reports on protein proteolytic enzyme or reagent cleavage sites
epestfind | Finds PEST motifs as potential proteolytic cleavage sites
fuzzpro | Search for patterns in protein sequences
fuzztran | Search for patterns in protein sequences (translated)
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences
oddcomp | Identify proteins with specified sequence word composition
patmatdb | Searches protein sequences with a sequence motif
patmatmotifs | Scan a protein sequence with motifs from the PROSITE database
pepcoil | Predicts coiled coil regions in protein sequences
preg | Regular expression search of protein sequence(s)
pscan | Scans protein sequence(s) with fingerprints from the PRINTS database
sigcleave | Reports on signal cleavage sites in a protein sequence

## Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Original program "ANTIGENIC" by Peter Rice (EGCG 1991) Peter Rice (pmr © ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## 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

None