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JACIII Vol.11 No.9 pp. 1129-1135
doi: 10.20965/jaciii.2007.p1129
(2007)

Paper:

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

Shinji Chiba* and Ken Sugawara**

*Department of Information Engineering, Sendai National College of Technology, 4-16-1 Ayashi-chuou, Aoba-ku, Sendai 989-3128, Japan

**Department of Information Science, Tohoku Gakuin University, 2-1-1 Tenjinzawa, Izumi-ku, Sendai 981-3193, Japan

Received:
December 12, 2006
Accepted:
July 17, 2007
Published:
November 20, 2007
Creative Commons License
Keywords:
amino acid sequence, motif, pair-wise alignment, finite state automaton, estimation of protein function
Abstract
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.
Cite this article as:
S. Chiba and K. Sugawara, “Estimation of Protein Function Using Optimized Finite State Automaton Based on Accumulated Amino Acid Residue Scores,” J. Adv. Comput. Intell. Intell. Inform., Vol.11 No.9, pp. 1129-1135, 2007.
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