Hardness Results on Local Multiple Alignment of Biological Sequences
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概要
- 論文の詳細を見る
This paper studies the local multiple alignment problem, which is, given protein or DNA sequences, to locate a region (i.e., a substring) of fixed length from each sequence so that the score determined from the set of regions is optimized. We consider the following scoring schemes: the relative entropy score (i.e., average information content), the sum-of-pairs score and a relative entropy-like score introduced by Li, et al. We prove that multiple local alignment is NP-hard under each of these scoring schemes. In particular, we prove that multiple local alignment is APX-hard under relative entropy scoring. It implies that unless P=NP there is no polynomial time algorithm whose worst case approximation error can be arbitrarily specified (precisely, a polynomial time approximation scheme). Several related theoretical results are also provided.
- 一般社団法人情報処理学会の論文
- 2007-03-15
著者
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Arimura Hiroki
Graduate School Of Information Science And Technology Hokkaido University
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Akutsu Tatsuya
Kyoto Univ.
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Akutsu Tatsuya
Bioinformatics Center Institute For Chemical Research Kyoto University
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Shimozono Shinichi
Department of Control Engineering and Science, Kyushu Institute of Technology
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Shimozono Shinichi
Department Of Artificial Intelligence Kyushu Institute Of Technology
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Akutsu Tatsuya
Bioinformatics Center Inst. For Chemical Res. Kyoto Univ.
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