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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 437 indices in release

of the database.

The EMBOSS programs pepwindow and pepwindowall plot hydrophobicity using the data from an Aaindex entry. If Aaindex is installed these programs can plot the other amino acid properties.

Aaindex can be obtained via anonymous FTP.3.14

Aaindex is integrated with EMBOSS using the program aaindexextract

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

The AAINDEX database is now integrated with EMBOSS.

Peter Rice 2007-04-26