Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries

  • Authors:

  • Jacek BłAewicz;Piotr Formanowicz;Marta Kasprzak;Wojciech T. Markiewicz;Aleksandra Wiercz

  • Affiliations:

  • Institute of Computing Science, Poznań University of Technology, Piotrowo 3A, 60-965 Poznań, Poland and Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, ...;Institute of Computing Science, Poznań University of Technology, Piotrowo 3A, 60-965 Poznań, Poland and Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, ...;Institute of Computing Science, Poznań University of Technology, Piotrowo 3A, 60-965 Poznań, Poland and Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, ...;Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland;Institute of Computing Science, Poznań University of Technology, Piotrowo 3A, 60-965 Poznań, Poland

  • Venue:
  • Computational Biology and Chemistry
  • Year:
  • 2004

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Abstract

In this paper, a problem of isothermic DNA sequencing by hybridization (SBH) is considered. In isothermic SBH a new type of oligonucleotide libraries is used. The library consists of oligonucleotides of different lengths depending on an oligonucleotide content. It is assumed that every oligonucleotide in such a library has an equal melting temperature. Each nucleotide adds its increment to the oligonucleotide temperature and it is assumed that A and T add 2^oC and C and G add 4^oC. The hybridization experiment using isothermic libraries should provide data with a lower number of errors due to an expected similarity of melting temperatures. From the computational point of view the problem of isothermic DNA sequencing with errors is hard, similarly like its classical counterpart. Hence, there is a need for developing heuristic algorithms that construct good suboptimal solutions. The aim of the paper is to propose a heuristic algorithm based on tabu search approach. The algorithm solves the problem with both positive and negative errors. Results of an extensive computational experiment are presented, which prove the high quality of the proposed method.