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The function of unknown proteins is currently most  effective determined by retrieving similar known sequences. Some effective  techniques involve sequence retrieval. We propose retrieval using a finite  state automaton (FSA). The FSA is created with accumulated amino acid  residue scores that express a property of a protein family. We  calculate the similarity of known and unknown protein  sequences using the FSA and used it to determine protein functions.  To improve accuracy, we optimized the FSA using a genetic algorithm. Results  from determining protein functions indicated that our proposal was superior  to general motif analysis.

Estimation of Protein Function Using Optimized Finite State Automaton Based on Accumulated Amino Acid Residue Scores