
                              aaindexextract 
                                      
   
   
Function

   Extract data from AAINDEX
   
Description

   aaextractindex extracts information from the AAINDEX database for use
   by pepwindow and pepwindowall
   
   AAINDEX is a database of properties of amino acids. See references [1]
   [2] [3].
   
   The programs pepwindow and pepwindowall normally use the standard
   EMBOSS data file 'Enakai.dat' by default, but you can set their
   '-data' qualifier to use any of the files produced by aaextractindex
   from the AAINDEX database.
   
   The AAINDEX database file 'aaindex1' can be downloaded from the
   AAINDEX site: ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1
   
Usage

   Here is a sample session with aaindexextract:

% aaindexextract
Extract data from AAINDEX
Full pathname of file aaindex1: ~/aaindex1

Command line arguments

   Standard (Mandatory) qualifiers:
  [-infile]            infile     Full pathname of file aaindex1

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   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
   [-infile]
   (Parameter 1) Full pathname of file aaindex1 Input file Required
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)
   
Input file format

   The AAINDEX database file 'aaindex1' can be downloaded from the
   AAINDEX site: ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/
   
Output file format

   One file for every entry in the AAINDEX database is created in the
   EMBOSS standard 'data/AAINDEX' directory. For example, the file
   'cham830102':
   
H CHAM830102
D A parameter defined from the residuals obtained from the best correlation
  of the Chou-Fasman parameter of beta-sheet (Charton-Charton, 1983)
R LIT:0907093b PMID:6876837
A Charton, M. and Charton, B.
T The dependence of the Chou-Fasman parameters on amino acid side chain
  structure
J J. Theor. Biol. 111, 447-450 (1983)
* (Pro !)
C
I   A/L    R/K    N/M    D/F    C/P    Q/S    E/T    G/W    H/Y    I/V
   -0.118  0.124  0.289  0.048  0.083 -0.105 -0.245  0.104  0.138  0.230
   -0.052  0.032 -0.258  0.015  0.     0.225  0.166  0.158  0.094  0.513
//

Data files

   None.
   
Notes

   If aaindexextract tries to write the data to an unexpected location
   you can explicitly set the location of the EMBOSS data directory by
   putting the line:
   
   ENV EMBOSS_DATA /path/to/the/EMBOSS/data/directory
   in the EMBOSS emboss.default file.
   
   (Where '/path/to/the/EMBOSS/data/directory' is the location of your
   EMBOSS data as unpacked from the distribution file.)
   
References

    1. Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino
       acid indices for prediction of protein structure and function.
       Protein Eng. 2, 93-100 (1988). [UI:89221001]
    2. Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and
       mutation matrices for sequence comparison and structure prediction
       of proteins. Protein Eng. 9, 27-36 (1996). [UI:96272030]
    3. Kawashima, S., Ogata, H., and Kanehisa, M.; AAindex: amino acid
       index database. Nucleic Acids Res. 27, 368-369 (1999).
       [UI:99063742]
       
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name Description
   cutgextract Extract data from CUTG
   printsextract Extract data from PRINTS
   prosextract Builds the PROSITE motif database for patmatmotifs to
   search
   rebaseextract Extract data from REBASE
   tfextract Extract data from TRANSFAC
   
   The programs pepwindow and pepwindowall normally use the standard
   EMBOSS data file 'Enakai.dat' by default, but you can set their
   '-data' qualifier to use any of the files produced by aaextractindex.
   
Author(s)

   Peter Rice (pmr © ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
   
History

   Written (25 June 2002) - Peter Rice
   
Target users

   This program is intended to be used by administrators responsible for
   software and database installation and maintenance.
   
Comments
