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Bioinformatics Advance Access published online on March 3, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti371
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 16, 2004
Revised February 21, 2005
Accepted March 1, 2005

Article

The Mutated Subsequence Problem and locating conserved genes

H. L. Chan 1, T. W. Lam 1, W. K. Sung 2, Prudence W. H. Wong 3, S. M. Yiu 1, and X. Fan 1

1 Department of Computer Science, University of Hong Kong, Hong Kong; supported in part by Hong Kong RGC Grant HKU-7139/04E
2 Department of Computer Science, National University of Singapore, Singapore
3 Department of Computer Science, University of Liverpool, UK


  Abstract

Motivation: For the purpose of locating conserved genes in a whole genome scale, this paper proposes a new structural optimization problem called the Mutated Subsequence Problem, which gives consideration to possible mutations between two species (in the form of reversals and transpositions) when comparing the genomes.

Results: A practical algorithm called MSS is devised to solve this optimization problem, and it has been evaluated using different pairs of human and mouse chromosomes, and different pairs of virus genomes of Baculovirdae. MSS is found to be effective and efficient; in particular, MSS can reveal over 90% of the conserved genes of human and mouse that have been reported in the literature. When compared to existing software MUMmer (Delcher et al., 2002; Kurtz et al., 2004) and MaxMinCluster (Wong et al., 2004), MSS uncovers 14% and 7% more genes on average, respectively. Furthermore, this paper shows a hybrid approach to integrate MUMmer or MaxMinCluster with MSS, which has better performance and reliability.

Availability: http://www.cs.hku.hk/~mss/.


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