[Owl-devel] Aminoacid reduced alphabets

Jose M. Duarte jose.m.duarte at gmail.com
Wed Jun 2 10:37:15 EDT 2010


I've added to the AminoAcid enum fields to store aminoacid reduced alphabet
classes and added the data for alphabets of 15, 10, 8, 6, 4 and 2 groups.
These are taken from Murphy et al. 2000 Protein Engineering and the 6-groups
one from Mirny and Shakhnovich 1999 JMB.

I am using those to calculate sequence entropies based on different
alphabets (see MultipleSequenceAlignment.getColumnEntropy) but somebody
might find them useful for something else.

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