Reduced.php

Reduced (redundant or simplified) alphabets are used to represent protein sequences using an alternative alphabet which lumps together several amino- acids into one letter, based on physico-chemical traits. For example, all the aliphatics (I,L,V) are usually quite interchangeable, so many sequence studies group them into one letter. Examples of reduced alphabets are available in{ http{//viscose.ifg.uni- muenster.de/html/alphabets.html

Bio.utils.reduce_sequence is used to take a Protein alphabet, and reduce it using one of the tables here, or a user-defined table. The Murphy tables are from here{ Murphy L.R., Wallqvist A, Levy RM. (2000) Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng. 13 (3){ 149-152

• author: Port from Bio::Python
• author: Mark Brooks <markabrooks@users.sourceforge.net>
• version: 0.8.2