Using a Java Based Program to Produce Reduced Amino Acid Alphabet Versions of Query Sequences and Databases

<p>Reduced amino acid alphabets are used to show similarity in sequence between two proteins that may not otherwise be detected. This can occur if slight changes or mutations have occurred over time through evolution and divergence of species. In this case the structure would remain similar, but the sequence would appear to be much different. It is important to explore different methods in which to determine the reduced amino acid alphabet that produces the most accurate results. Here we describe a program we created to convert individual protein sequences and entire databases to a user-defined reduced amino acid alphabet. An optimal reduced alphabet would need to conserve the fold of the original protein while also showing similarities in alignments that were not previously shown. Through the use of this Java-based program developed and BLAST we have begun to explore and make easier the use of reduced amino acid alphabets.