[Biopython-dev] aaindex1

Iddo Friedberg idoerg at burnham.org
Fri Apr 2 13:32:05 EST 2004

Hi all,

I wrote a module for parsing the aaindex1 database. From the aaindex1 
README file:
'An amino acid index is a set of 20 numerical values representing any
of the different physicochemical and biological properties of amino
acids.  The AAindex1 section of the Amino Acid Index Database is a
collection of published indices together with the result of cluster
analysis using the correlation coefficient as the distance between
two indices.  This section currently contains 494 indices.'

See http://www.genome.ad.jp/dbget/aaindex.html for details. aaindex1 
file may be
downloaded from

This module contains the following classes:
AAIndex1Record: holds the information from a single aaindex1 entry
AAIndex1Reader: parses the aaindex1 file

and one ustility which reads the aaindex1 file and returns a dictionary 
of entries.

Should I open a new directory under Bio/AAIndex1, or is there a more 
appropriate place for this?


Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930

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