antigenic.txt

emboss的linux版本的源代码

                                 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 protein sequence(s): tsw:act1_fugru
Minimum length of antigenic region [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 protein sequence(s): tsw:act1_fugru
Minimum length of antigenic region [6]: 
Output report [act1_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
   -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

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: Sat 15 Jul 2006 12:00:00
# Commandline: antigenic
#    -sequence tsw:act1_fugru
# 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