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Hidden Markov Models for Unaligned DNA Sequence Comparison
James Cook University, Townsville, QLD 4811, Australia..ORCID iD: 0000-0002-4255-5130
University of Applied Sciences Weihenstephan Weihenstephan, 85350 Freising, Germany.
Nathan Campus, Griffith University, QLD 4111, Australia..
2005 (English)In: WSEAS Transactions on Biology and Biomedicine, Vol. 2, 64-69 p.Article in journal (Refereed) Published
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Abstract [en]

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 set of 34 complete mammalian mtDNA genomes. The phylogenetic tree derived from the second experiment shows reasonable evolutionary relationships between these species.

Place, publisher, year, edition, pages
2005. Vol. 2, 64-69 p.
Keyword [en]
Sequence comparison, Hidden Markov models, Kullback-Leibler divergence.
National Category
Bioinformatics and Systems Biology
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URN: urn:nbn:se:liu:diva-125057OAI: oai:DiVA.org:liu-125057DiVA: diva2:902700
Available from: 2016-02-12 Created: 2016-02-12 Last updated: 2016-02-24

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Pham, Tuan D
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