Dynamic neighborhood searches for thermodynamically designing DNA sequence

Suguru Kawashimo, Hirotaka Ono, Kunihiko Sadakane, Masafumi Yamashita

研究成果: 著書/レポートタイプへの貢献会議での発言

10 引用 (Scopus)

抄録

We present a local search based algorithm designing DNA short-sequence sets satisfying thermodynamical constraints about minimum free energy (MFE) criteria. In DNA12, Kawashimo et al. propose a dynamic neighborhood search algorithm for the sequence design under hamming distance based constraints, where an efficient search is achieved by dynamically controlling the neighborhood structures. Different from the hamming distance based constraints, the thermodynamical constraints are generally difficult to handle in local-search type algorithms. This is because they require a large number of evaluations of MFE to find an improved solution, but the definition of MFE itself contains time-consuming computation. In this paper, we introduce techniques to reduce such time-consuming evaluations of MFE, by which the proposed dynamic neighborhood search strategy become applicable to the thermodynamical constraints in practice. In computational experiments, our algorithm succeeded in generating better sequence sets for many constraints than exiting methods.

元の言語英語
ホスト出版物のタイトルDNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers
ページ130-139
ページ数10
DOI
出版物ステータス出版済み - 8 27 2008
イベント13th International Meeting on DNA Computing, DNA13 - Memphis, TN, 米国
継続期間: 6 4 20076 8 2007

出版物シリーズ

名前Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
4848 LNCS
ISSN(印刷物)0302-9743
ISSN(電子版)1611-3349

その他

その他13th International Meeting on DNA Computing, DNA13
米国
Memphis, TN
期間6/4/076/8/07

Fingerprint

Neighborhood Search
DNA sequences
DNA Sequence
Free energy
Hamming distance
Free Energy
Hamming Distance
Local Search
DNA
Evaluation
Search Strategy
Computational Experiments
Search Algorithm
Experiments

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

これを引用

Kawashimo, S., Ono, H., Sadakane, K., & Yamashita, M. (2008). Dynamic neighborhood searches for thermodynamically designing DNA sequence. : DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers (pp. 130-139). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 巻数 4848 LNCS). https://doi.org/10.1007/978-3-540-77962-9_13

Dynamic neighborhood searches for thermodynamically designing DNA sequence. / Kawashimo, Suguru; Ono, Hirotaka; Sadakane, Kunihiko; Yamashita, Masafumi.

DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers. 2008. p. 130-139 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 巻 4848 LNCS).

研究成果: 著書/レポートタイプへの貢献会議での発言

Kawashimo, S, Ono, H, Sadakane, K & Yamashita, M 2008, Dynamic neighborhood searches for thermodynamically designing DNA sequence. : DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 巻. 4848 LNCS, pp. 130-139, 13th International Meeting on DNA Computing, DNA13, Memphis, TN, 米国, 6/4/07. https://doi.org/10.1007/978-3-540-77962-9_13
Kawashimo S, Ono H, Sadakane K, Yamashita M. Dynamic neighborhood searches for thermodynamically designing DNA sequence. : DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers. 2008. p. 130-139. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-540-77962-9_13
Kawashimo, Suguru ; Ono, Hirotaka ; Sadakane, Kunihiko ; Yamashita, Masafumi. / Dynamic neighborhood searches for thermodynamically designing DNA sequence. DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers. 2008. pp. 130-139 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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