aaindexextract extracts amino acid property data from the AAINDEX database (see references 1, 2 and 3). One file for every amino acid property is created in the EMBOSS data directory data/AAINDEX. Each file corresponds to a single entry in the file aindex1 of the AAINDEX database.
The aaindexextract output files files may be used by any program that uses amino acid property data. For example, pepwindow and pepwindowall will take any one of these files if their -data qualifier is set to an appropriate file name. By default however these programs will use the standard EMBOSS data file Enakai.dat.
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AAINDEX is a database of biochemical and physicochemical properties of amino acids and pairs of amino acids. aaindex1 for properties of each of the 20 single amino acids, aaindex2 for amino acid mutation matrices and aaindex3 for the amino-acid pair-wise contact potentials. All data are derived from the published literature. The file aaindex1 is required by aaindexextract and can be downloaded from the AAINDEX site: ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1.
aaindexextract will write to the EMBOSS data directory data/AAINDEX. If you cannot find the output files then it is likely the data directory has been set to somewhere other than expected. To set explicitly the location of the EMBOSS data directory add the following to your emboss.default file:
ENV EMBOSS_DATA /path/to/the/EMBOSS/data/directory
Where /path/to/the/EMBOSS/data/directory is the location of your EMBOSS data as unpacked from the distribution file.
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.