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|
<HTML>
<HEAD>
<TITLE>
EMBOSS: antigenic
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
antigenic
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Finds antigenic sites in proteins
<H2>
Description
</H2>
Antigenic predicts potentially antigenic regions of a protein
sequence, using the method of Kolaskar and Tongaonkar.
<p>
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.
<H2>
Usage
</H2>
<b>Here is a sample session with antigenic</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>antigenic </b>
Finds antigenic sites in proteins
Input protein sequence(s): <b>tsw:actb1_fugru</b>
Minimum length of antigenic region [6]: <b></b>
Output report [actb1_fugru.antigenic]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<p>
<b>Example 2</b>
<p>
By using the '-rformat gff' qualifier, a GFF file of the predicted regions can be produced.
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>antigenic -rformat gff </b>
Finds antigenic sites in proteins
Input protein sequence(s): <b>tsw:actb1_fugru</b>
Minimum length of antigenic region [6]: <b></b>
Output report [actb1_fugru.antigenic]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#output.2">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
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
-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 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 dying program messages
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>Protein sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-minlen</td>
<td>Minimum length of antigenic region</td>
<td>Integer from 1 to 50</td>
<td>6</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output report file name</td>
<td>Report output file</td>
<td><i><*></i>.antigenic</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
The input sequence can be one or more protein sequences.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tsw:actb1_fugru' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:actb1_fugru</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
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
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<p>
The output is a standard EMBOSS report file.
<p>
The results can be output in one of several styles by using the
command-line qualifier <b>-rformat xxx</b>, 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
<p>
See:
<A href="http://emboss.sf.net/docs/themes/ReportFormats.html">
http://emboss.sf.net/docs/themes/ReportFormats.html</A>
for further information on report formats.
<p>
By default <b>antigenic</b> writes a 'motif' report file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: actb1_fugru.antigenic</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: antigenic
# Rundate: Sun 15 Jul 2007 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
(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
<font color=red> [Part of this file has been deleted for brevity]</font>
(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
#---------------------------------------
#---------------------------------------
</pre>
</td></tr></table><p>
<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: actb1_fugru.antigenic</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
##gff-version 2.0
##date 2006-07-15
##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"
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
Antigenic uses a data file called <em>Eantigenic.dat</em>.
<p>
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.
<p>
To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
<pre>
% embossdata -fetch -file Exxx.dat
</pre>
<p>
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".
<p>
The directories are searched in the following order:
<ul>
<li> . (your current directory)
<li> .embossdata (under your current directory)
<li> ~/ (your home directory)
<li> ~/.embossdata
</ul>
<p>
<p>
Here is the default <em>Eantigenic.dat</em> file:
<pre>
# 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
</pre>
<H2>
Notes
</H2>
<H2>
References
</H2>
<ol>
<li>
Kolaskar,AS and Tongaonkar,PC (1990).
A semi-empirical method for prediction of antigenic determinants
on protein antigens.
FEBS Letters 276: 172-174.
<li>
Parker,JMR, Guo,D and Hodges,RS (1986).
Biochemistry 25: 5425-5432.
</ol>
<H2>
Warnings
</H2>
The program will warn you if the sequence is not a protein or has
ambiguity codes.
<H2>
Diagnostic Error Messages
</H2>
<H2>
Exit status
</H2>
It exits with status 0, unless a region is badly constructed.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="digest.html">digest</a></td>
<td>Protein proteolytic enzyme or reagent cleavage digest</td>
</tr>
<tr>
<td><a href="epestfind.html">epestfind</a></td>
<td>Finds PEST motifs as potential proteolytic cleavage sites</td>
</tr>
<tr>
<td><a href="fuzzpro.html">fuzzpro</a></td>
<td>Protein pattern search</td>
</tr>
<tr>
<td><a href="fuzztran.html">fuzztran</a></td>
<td>Protein pattern search after translation</td>
</tr>
<tr>
<td><a href="helixturnhelix.html">helixturnhelix</a></td>
<td>Report nucleic acid binding motifs</td>
</tr>
<tr>
<td><a href="oddcomp.html">oddcomp</a></td>
<td>Find protein sequence regions with a biased composition</td>
</tr>
<tr>
<td><a href="patmatdb.html">patmatdb</a></td>
<td>Search a protein sequence with a motif</td>
</tr>
<tr>
<td><a href="patmatmotifs.html">patmatmotifs</a></td>
<td>Search a PROSITE motif database with a protein sequence</td>
</tr>
<tr>
<td><a href="pepcoil.html">pepcoil</a></td>
<td>Predicts coiled coil regions</td>
</tr>
<tr>
<td><a href="preg.html">preg</a></td>
<td>Regular expression search of a protein sequence</td>
</tr>
<tr>
<td><a href="pscan.html">pscan</a></td>
<td>Scans proteins using PRINTS</td>
</tr>
<tr>
<td><a href="sigcleave.html">sigcleave</a></td>
<td>Reports protein signal cleavage sites</td>
</tr>
</table>
<!--
Add any comments about other associated programs (to prepare
data files?) that seealso doesn't find.
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<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<p>
Original program "ANTIGENIC" by Peter Rice (EGCG 1991)
Peter Rice (pmr © ebi.ac.uk)
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
<p>
Completed 9th March 1999
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
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