aaindexextract

Function

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

Command line arguments


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 'kytj820101':

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.

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)

History

Target users

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