Speeding up local-search type algorithms for designing DNA sequences under thermodynamical constraints

Suguru Kawashimo, Yen Kaow Ng, Hirotaka Ono, Kunihiko Sadakane, Masafumi Yamashita

研究成果: Chapter in Book/Report/Conference proceedingConference contribution

4 被引用数 (Scopus)

抄録

We present general techniques to speed up local search type algorithms for designing DNA sequences which satisfy thermodynamical constraints based on the minimum free energy (MFE) criteria. MFE based constraints are generally difficult to handle in local search type algorithms, since these algorithms typically require a large number of time-consuming calculations of MFE to find an improved solution. In this paper, we introduce general techniques to reduce such calculations of MFE. The ideas are based on the reuse of MFE computations and fast approximation of MFE, both of which fit the nature of local search type algorithms. In computational experiments, our techniques succeeded in speeding up typical local search type algorithms without degenerating the original performance of the algorithms.

本文言語英語
ホスト出版物のタイトルDNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers
ページ168-178
ページ数11
5347 LNCS
DOI
出版ステータス出版済み - 11 27 2009
イベント14th International Meeting on DNA Computing, DNA14 - Prague, チェコ共和国
継続期間: 6 2 20086 9 2008

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)
5347 LNCS
ISSN(印刷版)0302-9743
ISSN(電子版)1611-3349

その他

その他14th International Meeting on DNA Computing, DNA14
国/地域チェコ共和国
CityPrague
Period6/2/086/9/08

All Science Journal Classification (ASJC) codes

  • 理論的コンピュータサイエンス
  • コンピュータ サイエンス(全般)

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