Soft Computing Approach to the Analysis of the Amino Acid Similarity Matrices

Abstract

Amino acid similarity matrices are used for protein sequence compar- ison. A new method for studying connections between amino acid properties and similarity matrices is proposed. A representation of the amino acid similarity ma- trices, by means of the equivalence classes between amino acids, is proposed. It is shown that mappings between these equivalence classes and contiguous subsets of the amino acid property space are possible. These mappings are consistent between equivalence classes. There is a possibility of practical applications of this method in sequence similarity searches