antigenic.txt

emboss的linux版本的源代码

(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


  [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 2006-07-15
##Type Protein ACT1_FUGRU
ACT1_FUGRU      antigenic       region  214     222     1.207   +       .
Sequence "ACT1_FUGRU.1" ; note "*pos 218"
ACT1_FUGRU      antigenic       region  131     145     1.187   +       .
Sequence "ACT1_FUGRU.2" ; note "*pos 137"
ACT1_FUGRU      antigenic       region  5       12      1.166   +       .
Sequence "ACT1_FUGRU.3" ; note "*pos 8"
ACT1_FUGRU      antigenic       region  27      38      1.164   +       .
Sequence "ACT1_FUGRU.4" ; note "*pos 32"
ACT1_FUGRU      antigenic       region  160     183     1.136   +       .
Sequence "ACT1_FUGRU.5" ; note "*pos 173"
ACT1_FUGRU      antigenic       region  367     372     1.135   +       .
Sequence "ACT1_FUGRU.6" ; note "*pos 372"
ACT1_FUGRU      antigenic       region  93      108     1.116   +       .
Sequence "ACT1_FUGRU.7" ; note "*pos 103"
ACT1_FUGRU      antigenic       region  295     301     1.113   +       .
Sequence "ACT1_FUGRU.8" ; note "*pos 296"
ACT1_FUGRU      antigenic       region  256     266     1.110   +       .
Sequence "ACT1_FUGRU.9" ; note "*pos 264"
ACT1_FUGRU      antigenic       region  336     352     1.107   +       .
Sequence "ACT1_FUGRU.10" ; note "*pos 347"
ACT1_FUGRU      antigenic       region  62      76      1.102   +       .
Sequence "ACT1_FUGRU.11" ; note "*pos 68"
ACT1_FUGRU      antigenic       region  232     250     1.086   +       .
Sequence "ACT1_FUGRU.12" ; note "*pos 245"
ACT1_FUGRU      antigenic       region  327     332     1.083   +       .
Sequence "ACT1_FUGRU.13" ; note "*pos 330"
ACT1_FUGRU      antigenic       region  317     323     1.074   +       .
Sequence "ACT1_FUGRU.14" ; note "*pos 320"
ACT1_FUGRU      antigenic       region  186     192     1.068   +       .
Sequence "ACT1_FUGRU.15" ; note "*pos 191"
ACT1_FUGRU      antigenic       region  40      46      1.066   +       .
Sequence "ACT1_FUGRU.16" ; note "*pos 43"
ACT1_FUGRU      antigenic       region  269     275     1.045   +       .
Sequence "ACT1_FUGRU.17" ; note "*pos 269"
ACT1_FUGRU      antigenic       region  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

    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         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