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Bioinformatics Advance Access originally published online on April 8, 2004
Bioinformatics 2004 20(14):2181-2188; doi:10.1093/bioinformatics/bth202
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Bioinformatics 20(14) © Oxford University Press 2004; all rights reserved.

Probabilistic nucleotide assembling method for sequencing by hybridization

Takaho A. Endo

Division of Molecular Life Sciences, Department of Genetic Information, School of Medicine, Tokai University, Bouseidai, Isehara, Kanagawa, 259-1193, Japan

Received on July 14, 2003; revised on October 10, 2003; accepted on February 4, 2004
Advance Access Publication April 8, 2004

Motivation: Developing a new method of assembling small sequences based on sequencing by hybridization with many positive and negative faults. First, an interpretation of a generic traveling salesman problem is provided (i.e. finding the shortest route for visiting many cities), using genetic algorithms. Second, positive errors are excluded before assembly by a sanitization process.

Results: The present method outperforms those described in previous studies, in terms of both time and accuracy.

Availability: http://kamit.med.u-tokai.ac.jp/~takaho/sbh/index.html

Contact: endo{at}genetix-h.com


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