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Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries.

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 degrees C and C and G add 4 degrees C. 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.

journal_name

Comput Biol Chem

journal_title

Computational biology and chemistry

authors

Błazewicz J,Formanowicz P,Kasprzak M,Markiewicz WT,Swiercz A

doi

10.1016/j.compbiolchem.2003.12.002

keywords:

subject

Has Abstract

pub_date

2004-02-01 00:00:00

pages

11-9

issue

1

eissn

1476-9271

issn

1476-928X

pii

S1476927103001002

journal_volume

28

pub_type

杂志文章

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