                                  antigenic



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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

Finds antigenic sites in proteins
Version: EMBOSS:6.2.0

   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 and exit. 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
   -version            boolean    Report version number and exit


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   16-JUN-2009, entry version 31.
DE   RecName: Full=Actin, cytoplasmic 1;
DE   AltName: Full=Beta-actin A;
DE   Contains:
DE     RecName: Full=Actin, cytoplasmic 1, N-terminally processed;
GN   Name=actba;
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, cytoskeleton.
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   HOVERGEN; P68142; -.
DR   OMA; P68142; EKMTQIL.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005856; C:cytoskeleton; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0005515; F:protein binding; IEA:InterPro.
DR   InterPro; IPR004000; Actin-like.
DR   InterPro; IPR004001; Actin_CS.
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.
PE   2: Evidence at transcript level;
KW   Acetylation; ATP-binding; Cytoplasm; Cytoskeleton; Methylation;
KW   Nucleotide-binding.
FT   CHAIN         1    375       Actin, cytoplasmic 1.
FT                                /FTId=PRO_0000367094.
FT   INIT_MET      1      1       Removed; alternate (By similarity).
FT   CHAIN         2    375       Actin, cytoplasmic 1, N-terminally
FT                                processed.
FT                                /FTId=PRO_0000000809.
FT   MOD_RES       1      1       N-acetylmethionine; in Actin, cytoplasmic
FT                                1; alternate (By similarity).
FT   MOD_RES       2      2       N-acetylglutamate; in Actin, cytoplasmic
FT                                1, N-terminally processed (By
FT                                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: Fri 15 Jan 2010 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 3
##sequence-region ACTB1_FUGRU 1 375
#!Date 2010-01-15
#!Type Protein
#!Source-version EMBOSS 6.2.0
ACTB1_FUGRU     antigenic       epitope 214     222     1.207   +       .
ID="ACTB1_FUGRU.1";note="*pos 218"
ACTB1_FUGRU     antigenic       epitope 131     145     1.187   +       .
ID="ACTB1_FUGRU.2";note="*pos 137"
ACTB1_FUGRU     antigenic       epitope 5       12      1.166   +       .
ID="ACTB1_FUGRU.3";note="*pos 8"
ACTB1_FUGRU     antigenic       epitope 27      38      1.164   +       .
ID="ACTB1_FUGRU.4";note="*pos 32"
ACTB1_FUGRU     antigenic       epitope 160     183     1.136   +       .
ID="ACTB1_FUGRU.5";note="*pos 173"
ACTB1_FUGRU     antigenic       epitope 367     372     1.135   +       .
ID="ACTB1_FUGRU.6";note="*pos 372"
ACTB1_FUGRU     antigenic       epitope 93      108     1.116   +       .
ID="ACTB1_FUGRU.7";note="*pos 103"
ACTB1_FUGRU     antigenic       epitope 295     301     1.113   +       .
ID="ACTB1_FUGRU.8";note="*pos 296"
ACTB1_FUGRU     antigenic       epitope 256     266     1.110   +       .
ID="ACTB1_FUGRU.9";note="*pos 264"
ACTB1_FUGRU     antigenic       epitope 336     352     1.107   +       .
ID="ACTB1_FUGRU.10";note="*pos 347"
ACTB1_FUGRU     antigenic       epitope 62      76      1.102   +       .
ID="ACTB1_FUGRU.11";note="*pos 68"
ACTB1_FUGRU     antigenic       epitope 232     250     1.086   +       .
ID="ACTB1_FUGRU.12";note="*pos 245"
ACTB1_FUGRU     antigenic       epitope 327     332     1.083   +       .
ID="ACTB1_FUGRU.13";note="*pos 330"
ACTB1_FUGRU     antigenic       epitope 317     323     1.074   +       .
ID="ACTB1_FUGRU.14";note="*pos 320"
ACTB1_FUGRU     antigenic       epitope 186     192     1.068   +       .
ID="ACTB1_FUGRU.15";note="*pos 191"
ACTB1_FUGRU     antigenic       epitope 40      46      1.066   +       .
ID="ACTB1_FUGRU.16";note="*pos 43"
ACTB1_FUGRU     antigenic       epitope 269     275     1.045   +       .
ID="ACTB1_FUGRU.17";note="*pos 269"
ACTB1_FUGRU     antigenic       epitope 51      57      1.034   +       .
ID="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:
# Kolaskar AS and Tongaonkar PC (1990) FEBS Letters 276:172-174
# "A semi-emipirical method for prediction of antigenic determinants
# on protein antigens"
#
# TABLE 1: Occurrence of amino acids in epitopes, proteins and on the surface,
#         and their antigenic propensity, A(p), values
#
# 169 antigenic determinants experimentally determined. Selected those 156
# which have less than 20 amino acids per determinant (total 2066 residues).
# Calculated f(Ag) as frequency of occurrence of each residue in antigenic
# determinants [f(Ag) = Epitope_occurrence/2066].
#
# Used Hydrophilicity, Accessibility and Flexibility of Parker JMR, Guo D,
# Hodges, RS (1986) Biochemistry 25:5425-5432. In a given protein, calculated
# average for each 7-mer and assigned values to central residue of 7-mer.
# Residue considered to be on the surface if any of the 7-mer values was above
# the average for the protein. Used these results to get f(s) frequency of
# occurrence of amino acids at the surface.
#
# Original table covers the 20 naturally occurring amino acids.
# Values for B, Z, X use weighted averages from Edayhoff.dat
# and are ignored when calculating totals
#
# Antigenic propensity column A(p) = f(Ag)/f(s)
#
# f(s) values below were back-calculated from the table in the paper
#
# Prediction algorithm:
#
# 1. calculate average propensity  for each overlapping 7-mer, assign to
#    central residue (i+3)
#
# 2. calculate average for whole protein A(p)av
#
# 3. (a) if average for whole protein >= 1.0 then all residues having
#         >= 1.0 are potentially antigenic.
#    (b) if average for whole protein <  1.0 then all residues having
#         > average for whole protein (??? paper has a mangled
#        formula here :-) are potentially antigenic.
#
# 4. Find 6-mers where all residues are selected by step 3 above
#
#                                               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
  B             107          334         410     0.052    0.062     0.827
  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
  X             118          306         453     0.057    0.057     1.025
  Y              71          158         245     0.034    0.029     1.161
  Z             119          342         433     0.058    0.064     0.916
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.

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 (c) 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 (c) ebi.ac.uk)
   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
