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Bioinformatics Advance Access originally published online on August 18, 2008
Bioinformatics 2008 24(20):2296-2302; doi:10.1093/bioinformatics/btn436
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison

Qi Dai *, Yanchun Yang and Tianming Wang

Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, China

*To whom correspondence should be addressed.


  Abstract

Motivation: Many proposed statistical measures can efficiently compare biological sequences to further infer their structures, functions and evolutionary information. They are related in spirit because all the ideas for sequence comparison try to use the information on the k-word distributions, Markov model or both. Motivated by adding k-word distributions to Markov model directly, we investigated two novel statistical measures for sequence comparison, called wre.k.r and S2.k.r.

Results: The proposed measures were tested by similarity search, evaluation on functionally related regulatory sequences and phylogenetic analysis. This offers the systematic and quantitative experimental assessment of our measures. Moreover, we compared our achievements with these based on alignment or alignment-free. We grouped our experiments into two sets. The first one, performed via ROC (receiver operating curve) analysis, aims at assessing the intrinsic ability of our statistical measures to search for similar sequences from a database and discriminate functionally related regulatory sequences from unrelated sequences. The second one aims at assessing how well our statistical measure is used for phylogenetic analysis. The experimental assessment demonstrates that our similarity measures intending to incorporate k-word distributions into Markov model are more efficient.

Availability: The software, data and supplement material are freely available at http://math.dlut.edu.cn/daiqi/mplusd.html.

Contact: daiailiu2004{at}yahoo.com.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Limsoon Wong

Received on April 15, 2008; revised on August 16, 2008; accepted on August 17, 2008

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