Hidden Markov models for unaligned DNA sequence comparison

Pham, Tuan D., Beck, Dominik, and Crane, Denis (2005) Hidden Markov models for unaligned DNA sequence comparison. WSEAS Transactions on Biology and Biomedicine, 2 (1). pp. 64-69.

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Comparison of similarity between sequences can provide information for inferring the function of a newly discovered sequence, and understanding the evolutionary relationships among genes, proteins, and entire species. This paper presents a technique for computing the similarity between unaligned DNA sequences. The computation is based on the Kullback-Leibler divergence of hidden Markov models. We used the data sets taken from the threonine operons of Escherichia coli K-12 and Shigella flexneri to test the proposed method. The result obtained agrees with an alignment-based method. We further tested the proposed method with a data ~et of 34 complete mammalian mtDNA genomes. The phylogenetic tree derived from the second experiment shows reasonable evolutionary relationships between these species.

Item ID: 14097
Item Type: Article (Research - C1)
ISSN: 1109-9518
Keywords: hidden Markov models; Kullback-Leibler divergence; sequence comparison
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Date Deposited: 03 Dec 2010 02:42
FoR Codes: 08 INFORMATION AND COMPUTING SCIENCES > 0899 Other Information and Computing Sciences > 089999 Information and Computing Sciences not elsewhere classified @ 100%
SEO Codes: 89 INFORMATION AND COMMUNICATION SERVICES > 8999 Other Information and Communication Services > 899999 Information and Communication Services not elsewhere classified @ 100%
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