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
- 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]
- 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]
- 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
Comments