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 nameDescription
cutgextractExtract data from CUTG
printsextractExtract data from PRINTS
prosextractBuilds the PROSITE motif database for patmatmotifs to search
rebaseextractExtract data from REBASE
tfextractExtract 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