EMBOSS: antigenic manual

antigenic

Function

Finds antigenic sites in proteins

Description

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

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. A semi-empirical method which makes use of physicochemical properties of amino acid residues and their frequencies of occurrence in experimentally known segmental epitopes was developed by Kolaskar and Tongaonkar to predict antigenic determinants on proteins. 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. This method is based on a single parameter and thus very simple to use.

Usage

Here is a sample session with antigenic


% antigenic 
Finds antigenic sites in proteins
Input sequence(s): tsw:act1_fugru
Minimum length [6]: 
Output report [act1_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 sequence(s): tsw:act1_fugru
Minimum length [6]: 
Output report [act1_fugru.antigenic]:

Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
   -minlen             integer    Minimum length
  [-outfile]           report     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
   -rusashow2           boolean    Show the full USA in the report

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write 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 deaths

Standard (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 report file name	Report output file
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:act1_fugru' is a sequence entry in the example protein database 'tsw'

Database entry: tsw:act1_fugru

ID   ACT1_FUGRU     STANDARD;      PRT;   375 AA.
AC   P53484;
DT   01-OCT-1996 (REL. 34, CREATED)
DT   01-OCT-1996 (REL. 34, LAST SEQUENCE UPDATE)
DT   01-OCT-1996 (REL. 34, LAST ANNOTATION UPDATE)
DE   ACTIN, CYTOPLASMIC 1 (BETA-ACTIN 1).
OS   FUGU RUBRIPES (JAPANESE PUFFERFISH) (TAKIFUGU RUBRIPES).
OC   EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; PISCES; GNATHOSTOMATA;
OC   OSTEICHTHYES; ACTINOPTERYGII; TETRAODONTIFORMES.
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE; 96275651.
RA   VENKATESH B., TAY B.H., ELGAR G., BRENNER S.;
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
CC       HELIX. EACH ACTIN CAN BIND TO 4 OTHERS.
CC   -!- SUBCELLULAR LOCATION: CYTOPLASMIC.
CC   -!- TISSUE SPECIFICITY: WIDELY DISTRIBUTED. NOT EXPRESSED IN SKELETAL
CC       MUSCLE.
CC   -!- IN VERTEBRATES 3 MAIN GROUPS OF ACTIN ISOFORMS, ALPHA, BETA AND
CC       GAMMA HAVE BEEN IDENTIFIED. THE ALPHA ACTINS ARE FOUND IN MUSCLE
CC       TISSUES AND ARE A MAJOR CONSTITUENT OF THE CONTRACTILE APPARATUS.
CC       THE BETA AND GAMMA ACTINS CO-EXISTS IN MOST CELL TYPES AS
CC       COMPONENTS OF THE CYTOSKELETON AND AS MEDIATORS OF INTERNAL CELL
CC       MOTILITY.
CC   -!- THERE ARE THREE DIFFERENT BETA-CYTOPLASMIC ACTINS IN FUGU
CC       RUBRIPES.
DR   EMBL; U37499; G1335821; -.
DR   PROSITE; PS00406; ACTINS_1; 1.
DR   PROSITE; PS00432; ACTINS_2; 1.
DR   PROSITE; PS01132; ACTINS_ACT_LIKE; 1.
KW   MULTIGENE FAMILY; STRUCTURAL PROTEIN; METHYLATION; ACETYLATION;
KW   CYTOSKELETON.
FT   PROPEP        1      1       REMOVED IN MATURE FORM (BY SIMILARITY).
FT   CHAIN         2    375       ACTIN, CYTOPLASMIC 1.
FT   MOD_RES       1      1       ACETYLATION (BY SIMILARITY).
FT   MOD_RES       2      2       ACETYLATION (BY SIMILARITY).
FT   MOD_RES      73     73       METHYLATION (BY SIMILARITY).
SQ   SEQUENCE   375 AA;  41766 MW;  3A0543DF CRC32;
     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: act1_fugru.antigenic

########################################
# Program: antigenic
# Rundate: Fri Jul 15 2005 12:00:00
# Report_format: motif
# Report_file: act1_fugru.antigenic
########################################

#=======================================
#
# Sequence: ACT1_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

(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

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

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

(6) Score 1.135 length 6 at residues 367->372
                *
 Sequence: PSIVHR
           |    |
         367    372


  [Part of this file has been deleted for brevity]

(11) Score 1.102 length 15 at residues 62->76
                 *
 Sequence: RGILTLKYPIEHGIV
           |             |
          62             76

(12) Score 1.086 length 19 at residues 232->250
                        *
 Sequence: SSSSLEKSYELPDGQVITI
           |                 |
         232                 250

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

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

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

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

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

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


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

Output files for usage example 2

File: act1_fugru.antigenic

##gff-version 2.0
##date 2005-07-15
##Type Protein ACT1_FUGRU
ACT1_FUGRU	antigenic	site	214	222	1.207	+	.	Sequence "ACT1_FUGRU.1" ; note "*pos 218"
ACT1_FUGRU	antigenic	site	131	145	1.187	+	.	Sequence "ACT1_FUGRU.2" ; note "*pos 137"
ACT1_FUGRU	antigenic	site	5	12	1.166	+	.	Sequence "ACT1_FUGRU.3" ; note "*pos 8"
ACT1_FUGRU	antigenic	site	27	38	1.164	+	.	Sequence "ACT1_FUGRU.4" ; note "*pos 32"
ACT1_FUGRU	antigenic	site	160	183	1.136	+	.	Sequence "ACT1_FUGRU.5" ; note "*pos 173"
ACT1_FUGRU	antigenic	site	367	372	1.135	+	.	Sequence "ACT1_FUGRU.6" ; note "*pos 372"
ACT1_FUGRU	antigenic	site	93	108	1.116	+	.	Sequence "ACT1_FUGRU.7" ; note "*pos 103"
ACT1_FUGRU	antigenic	site	295	301	1.113	+	.	Sequence "ACT1_FUGRU.8" ; note "*pos 296"
ACT1_FUGRU	antigenic	site	256	266	1.110	+	.	Sequence "ACT1_FUGRU.9" ; note "*pos 264"
ACT1_FUGRU	antigenic	site	336	352	1.107	+	.	Sequence "ACT1_FUGRU.10" ; note "*pos 347"
ACT1_FUGRU	antigenic	site	62	76	1.102	+	.	Sequence "ACT1_FUGRU.11" ; note "*pos 68"
ACT1_FUGRU	antigenic	site	232	250	1.086	+	.	Sequence "ACT1_FUGRU.12" ; note "*pos 245"
ACT1_FUGRU	antigenic	site	327	332	1.083	+	.	Sequence "ACT1_FUGRU.13" ; note "*pos 330"
ACT1_FUGRU	antigenic	site	317	323	1.074	+	.	Sequence "ACT1_FUGRU.14" ; note "*pos 320"
ACT1_FUGRU	antigenic	site	186	192	1.068	+	.	Sequence "ACT1_FUGRU.15" ; note "*pos 191"
ACT1_FUGRU	antigenic	site	40	46	1.066	+	.	Sequence "ACT1_FUGRU.16" ; note "*pos 43"
ACT1_FUGRU	antigenic	site	269	275	1.045	+	.	Sequence "ACT1_FUGRU.17" ; note "*pos 269"
ACT1_FUGRU	antigenic	site	51	57	1.034	+	.	Sequence "ACT1_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

References

Kolaskar,AS and Tongaonkar,PC (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Letters 276: 172-174.
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.

Program name	Description
digest	Protein proteolytic enzyme or reagent cleavage digest
epestfind	Finds PEST motifs as potential proteolytic cleavage sites
fuzzpro	Protein pattern search
fuzztran	Protein pattern search after translation
helixturnhelix	Report nucleic acid binding motifs
oddcomp	Find protein sequence regions with a biased composition
patmatdb	Search a protein sequence with a motif
patmatmotifs	Search a PROSITE motif database with a protein sequence
pepcoil	Predicts coiled coil regions
preg	Regular expression search of a protein sequence
pscan	Scans proteins using PRINTS
sigcleave	Reports protein signal cleavage sites

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

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: tsw:act1_fugru

Output file format

Output files for usage example

File: act1_fugru.antigenic

Output files for usage example 2

File: act1_fugru.antigenic

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments