Dynamic neighborhood searches for thermodynamically designing DNA sequence

Suguru Kawashimo, Hirotaka Ono, Kunihiko Sadakane, Masafumi Yamashita

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

10 Citations (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationDNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers
Pages130-139
Number of pages10
Volume4848 LNCS
DOIs
Publication statusPublished - Aug 27 2008
Event13th International Meeting on DNA Computing, DNA13 - Memphis, TN, United States
Duration: Jun 4 2007Jun 8 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4848 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other13th International Meeting on DNA Computing, DNA13
CountryUnited States
CityMemphis, TN
Period6/4/076/8/07

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)

Cite this

Kawashimo, S., Ono, H., Sadakane, K., & Yamashita, M. (2008). Dynamic neighborhood searches for thermodynamically designing DNA sequence. In DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers (Vol. 4848 LNCS, pp. 130-139). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 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. Vol. 4848 LNCS 2008. p. 130-139 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4848 LNCS).

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

Kawashimo, S, Ono, H, Sadakane, K & Yamashita, M 2008, Dynamic neighborhood searches for thermodynamically designing DNA sequence. in DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers. vol. 4848 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4848 LNCS, pp. 130-139, 13th International Meeting on DNA Computing, DNA13, Memphis, TN, United States, 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. In DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers. Vol. 4848 LNCS. 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. Vol. 4848 LNCS 2008. pp. 130-139 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
@inproceedings{6403ce323e4643ad893aec6e251827b4,
title = "Dynamic neighborhood searches for thermodynamically designing DNA sequence",
abstract = "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.",
author = "Suguru Kawashimo and Hirotaka Ono and Kunihiko Sadakane and Masafumi Yamashita",
year = "2008",
month = "8",
day = "27",
doi = "10.1007/978-3-540-77962-9_13",
language = "English",
isbn = "3540779612",
volume = "4848 LNCS",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
pages = "130--139",
booktitle = "DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers",

}

TY - GEN

T1 - Dynamic neighborhood searches for thermodynamically designing DNA sequence

AU - Kawashimo, Suguru

AU - Ono, Hirotaka

AU - Sadakane, Kunihiko

AU - Yamashita, Masafumi

PY - 2008/8/27

Y1 - 2008/8/27

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=49949096745&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=49949096745&partnerID=8YFLogxK

U2 - 10.1007/978-3-540-77962-9_13

DO - 10.1007/978-3-540-77962-9_13

M3 - Conference contribution

SN - 3540779612

SN - 9783540779612

VL - 4848 LNCS

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 130

EP - 139

BT - DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers

ER -