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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Abstract

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
Additional Information:	No current JCU email address available.
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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