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

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationDNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers
Pages168-178
Number of pages11
Volume5347 LNCS
DOIs
Publication statusPublished - Nov 27 2009
Event14th International Meeting on DNA Computing, DNA14 - Prague, Czech Republic
Duration: Jun 2 2008Jun 9 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5347 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other14th International Meeting on DNA Computing, DNA14
CountryCzech Republic
CityPrague
Period6/2/086/9/08

Fingerprint

DNA sequences
DNA Sequence
Local Search
Free energy
Free Energy
Computational Experiments
Reuse
Speedup
Approximation
Experiments

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Kawashimo, S., Kaow Ng, Y., Ono, H., Sadakane, K., & Yamashita, M. (2009). Speeding up local-search type algorithms for designing DNA sequences under thermodynamical constraints. In DNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers (Vol. 5347 LNCS, pp. 168-178). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5347 LNCS). https://doi.org/10.1007/978-3-642-03076-5_14

Speeding up local-search type algorithms for designing DNA sequences under thermodynamical constraints. / Kawashimo, Suguru; Kaow Ng, Yen; Ono, Hirotaka; Sadakane, Kunihiko; Yamashita, Masafumi.

DNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers. Vol. 5347 LNCS 2009. p. 168-178 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5347 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Kawashimo, S, Kaow Ng, Y, Ono, H, Sadakane, K & Yamashita, M 2009, Speeding up local-search type algorithms for designing DNA sequences under thermodynamical constraints. in DNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers. vol. 5347 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5347 LNCS, pp. 168-178, 14th International Meeting on DNA Computing, DNA14, Prague, Czech Republic, 6/2/08. https://doi.org/10.1007/978-3-642-03076-5_14
Kawashimo S, Kaow Ng Y, Ono H, Sadakane K, Yamashita M. Speeding up local-search type algorithms for designing DNA sequences under thermodynamical constraints. In DNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers. Vol. 5347 LNCS. 2009. p. 168-178. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-03076-5_14
Kawashimo, Suguru ; Kaow Ng, Yen ; Ono, Hirotaka ; Sadakane, Kunihiko ; Yamashita, Masafumi. / Speeding up local-search type algorithms for designing DNA sequences under thermodynamical constraints. DNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers. Vol. 5347 LNCS 2009. pp. 168-178 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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