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A Simulated Annealing Algorithm for Finding Consensus Sequences

Keith, Jonathan M, Adams, Peter, Bryant, Darryn, Kroese, Dirk P, Mitchelson, Keith R, Cochran, Duncan A., & Lala, Gita H. (2002) A Simulated Annealing Algorithm for Finding Consensus Sequences. Bioinformatics, 18(11), pp. 1494-1499.

Abstract

Motivation: A consensus sequence for a family of related sequences is, as the name suggests, a sequence that captures the features common to most members of the family. Consensus sequences are important in various DNA sequencing applications and are a convenient way to characterize a family of molecules. Results: This paper describes a new algorithm for finding a consensus sequence, using the popular optimization method known as simulated annealing. Unlike the conventional approach of finding a consensus sequence by first forming a multiple sequence alignment, this algorithm searches for a sequence that minimises the sum of pairwise distances to each of the input sequences. The resulting consensus sequence can then be used to induce a multiple sequence alignment. The time required by the algorithm scales linearly with the number of input sequences and quadratically with the length of the consensus sequence. We present results demonstrating the high quality of the consensus sequences and alignments produced by the new altorithm. For comparison, we also present similar results obtained using Clustal W. The new algorithm outperforms ClustalW in many cases. Availability: The software is made available upon request. Contact: jonathan@maths.uq.edu.au

Impact and interest:

25 citations in Scopus
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22 citations in Web of Science®

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ID Code: 8017
Item Type: Journal Article
Additional Information: For more information, please refer to the publisher's website (link above) or contact the author: j.keith@qut.edu.au
Additional URLs:
Subjects: Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > APPLIED MATHEMATICS (010200) > Biological Mathematics (010202)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Copyright Owner: Copyright 2002 Oxford University Press
Deposited On: 06 Jun 2007
Last Modified: 11 Aug 2011 01:19

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