Quantum algorithm for multiple alignment of amino acid sequences

Authors:
Satoshi Iriyama;Masanori Ohya
Affiliations:
Tokyo University of Science, Department of Information Science, Noda City, Chiba, Japan;Tokyo University of Science, Department of Information Science, Noda City, Chiba, Japan
Venue:
MCBC'09 Proceedings of the 10th WSEAS international conference on Mathematics and computers in biology and chemistry
Year:
2009

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Abstract

The alignment of genome sequences or amino acid sequences is one of fundamental operations for the study of life. Usual computational complexity for the multiple alignment of N sequences with common length L by dynamic programming is O(LN). This alignment is considered as one of the NP problems, so that it is desirable to find a nice algorithm of the multiple alignment. Thus in this paper we propose the quantum algorithm for the multiple alignment based on the works [7, 14] in which the NP complete problem was shown to be the P problem by means of quantum algorithm and chaos informarion dynamics.