Function estimation of protein using finite state automaton based on accumulated amino acid residue scores

Today, most effective method to estimate the function of unknown protein is to retrieve similar known sequences. There are some effective techniques for sequence retrieval to estimate protein functions. We propose a method to express the amino acid sequence by finite state automaton. At first, we introduce an accumulated amino acid residue score (ARS). Next, we introduce a finite state automaton (FSA) to describe the alignment of amino acid residues. Combining ARS and FSA, and we can calculate the similarity of known protein sequence and unknown one. We applied this method to a protein family and examined the efficiency of this method.