DNA sequence design by dynamic neighborhood searches

Suguru Kawashimo, Hirotaka Ono, Kunihiko Sadakane, Masafumi Yamashita

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

18 Citations (Scopus)

Abstract

We propose a local-search based algorithm to design DNA sequence sets that satisfy several combinatorial constraints about hamming-distance criteria. To deal with the constraints in the local search, we adopt elaborate (and dynamic) neighborhood search frameworks called the Variable Neighborhood Search (VNS) and the Variable Depth Search (VDS). Although our algorithm can deal with many types of hamming distance-based constraints and is easy to extend (e.g., also applicable for other constraints), in computational experiments, we succeeded in generating better sequence sets than the ones generated by exiting methods of more specified constraints.

Original languageEnglish
Title of host publicationDNA Computing - 12th International Meeting on DNA Computing, DNA12, Revised Selected Papers
Pages157-171
Number of pages15
Volume4287 LNCS
DOIs
Publication statusPublished - Dec 1 2006
Event12th International Meeting on DNA Computing, DNA12 - Seoul, Korea, Republic of
Duration: Jun 5 2006Jun 9 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4287 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other12th International Meeting on DNA Computing, DNA12
Country/TerritoryKorea, Republic of
CitySeoul
Period6/5/066/9/06

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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