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Title: The mutated subsequence problem and locating conserved genes
Authors: Chan, H.L.
Lam, T.W.
Sung, W.K. 
Wong, P.W.H.
Yiu, S.M.
Fan, X.
Issue Date: 2005
Citation: Chan, H.L., Lam, T.W., Sung, W.K., Wong, P.W.H., Yiu, S.M., Fan, X. (2005). The mutated subsequence problem and locating conserved genes. Bioinformatics 21 (10) : 2271-2278. ScholarBank@NUS Repository.
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 mutated subsequence algorithm (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 Baculoviridae. MSS is found to be effective and efficient; in particular, MSS can reveal >90% of the conserved genes of human and mouse that have been reported in the literature. When compared with existing softwares MUMmer and MaxMinCluster, 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. © The Author 2005. Published by Oxford University Press. All rights reserved.
Source Title: Bioinformatics
ISSN: 13674803
DOI: 10.1093/bioinformatics/bti371
Appears in Collections:Staff Publications

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