pepinfo.txt

emboss的linux版本的源代码

Output file format

   Graphs are written to the selected graphics device.

  Output files for usage example

  File: opsd_human.pepinfo

Printing out Tiny residues in OPSD_HUMAN from position 1 to 348

Position  Residue                       Result
       1       M                               0
       2       N                               0
       3       G                               1
       4       T                               1
       5       E                               0
       6       G                               1
       7       P                               0
       8       N                               0
       9       F                               0
      10       Y                               0
      11       V                               0
      12       P                               0
      13       F                               0
      14       S                               1
      15       N                               0
      16       A                               1
      17       T                               1
      18       G                               1
      19       V                               0
      20       V                               0
      21       R                               0
      22       S                               1
      23       P                               0
      24       F                               0
      25       E                               0
      26       Y                               0
      27       P                               0
      28       Q                               0
      29       Y                               0
      30       Y                               0
      31       L                               0
      32       A                               1
      33       E                               0
      34       P                               0
      35       W                               0
      36       Q                               0
      37       F                               0
      38       S                               1
      39       M                               0
      40       L                               0
      41       A                               1
      42       A                               1
      43       Y                               0
      44       M                               0
      45       F                               0
      46       L                               0
      47       L                               0


  [Part of this file has been deleted for brevity]

  301       Y                           0.500
  302       N                           0.549
  303       P                           0.633
  304       V                           0.636
  305       I                           0.553
  306       Y                           0.438
  307       I                           0.358
  308       M                           0.250
  309       M                           0.262
  310       N                          -0.172
  311       K                          -0.288
  312       Q                          -0.409
  313       F                          -0.409
  314       R                          -0.362
  315       N                          -0.281
  316       C                          -0.120
  317       M                           0.128
  318       L                           0.028
  319       T                           0.341
  320       T                           0.481
  321       I                           0.282
  322       C                           0.124
  323       C                           0.020
  324       G                           0.143
  325       K                           0.202
  326       N                          -0.051
  327       P                          -0.183
  328       L                          -0.298
  329       G                          -0.282
  330       D                          -0.136
  331       D                           0.020
  332       E                           0.001
  333       A                           0.003
  334       S                          -0.070
  335       A                          -0.137
  336       T                          -0.042
  337       V                          -0.042
  338       S                          -0.117
  339       K                          -0.117
  340       T                          -0.280
  341       E                          -0.154
  342       T                          -0.206
  343       S                          -0.172
  344       Q                           0.063
  345       V                           0.000
  346       A                           0.000
  347       P                           0.000
  348       A                           0.000



  Graphics File: pepinfo.ps

   [pepinfo results]

   The output file 'pepinfo.out' contains the coordinates from the
   graphs.

   For the first set of graphs, 9 sets of true/false values are written
   out. For the second set of graphs, 3 sets of hydrophobicity values are
   written.

Data files

   The physico-chemical properties of the residues are read from the
   EMBOSS data file 'Eaa_properties.dat'. This file can be copied into
   your current directory and inspected ot altered by using the
   application 'embossdata -fetch'. Another file can be specified using
   the qualifier '-aaproperties'.

   The hydropathy data of the residues are read from the EMBOSS data file
   'Eaa_hydropathy.dat'. This file can be copied into your current
   directory and inspected ot altered by using the application
   'embossdata -fetch'. Another file can be specified using the qualifier
   '-aahydropathy'.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by EMBOSS
   environment variable EMBOSS_DATA.

   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

Notes

   None.

References

    1. Kyte J, Doolittle RF A simple method for displaying the
       hydropathic character of a protein. J Mol Biol 1982 May
       5;157(1):105-132
    2. Sweet RM, Eisenberg D Correlation of sequence hydrophobicities
       measures similarity in three-dimensional protein structure. J Mol
       Biol 1983 Dec 25;171(4):479-488
    3. Eisenberg D, Weiss RM, Terwilliger TC. The helical hydrophobic
       moment: a measure of the amphiphilicity of a helix. Nature 1982
       Sep 23;299(5881):371-4

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name                         Description
   backtranambig Back translate a protein sequence to ambiguous codons
   backtranseq   Back translate a protein sequence
   charge        Protein charge plot
   checktrans    Reports STOP codons and ORF statistics of a protein
   compseq       Count composition of dimer/trimer/etc words in a sequence
   emowse        Protein identification by mass spectrometry
   freak         Residue/base frequency table or plot
   iep           Calculates the isoelectric point of a protein
   mwcontam      Shows molwts that match across a set of files
   mwfilter      Filter noisy molwts from mass spec output
   octanol       Displays protein hydropathy
   pepstats      Protein statistics
   pepwindow     Displays protein hydropathy
   pepwindowall  Displays protein hydropathy of a set of sequences

Author(s)

   Mark Faller (current e-mail address unknown)
   while he was with:
   HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

History

   Written (1999) - Mark Faller

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None