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Bioinformatics Advance Access published online on February 2, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp070
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Accurate Identification of Orthologous Segments among Multiple Genomes

Tsuyoshi Hachiya 1, Yasunori Osana 2, Kris Popendorf 1 and Yasubumi Sakakibara 1,*

1Department of Biosciences and Informatics, Keio University, Japan.
2Department of Computer and Informatics Science, Seikei University, Japan.

*To whom correspondence should be addressed. Mr. Tsuyoshi Hachiya, E-mail: hacchy{at}dna.bio.keio.ac.jp


  Abstract

Motivation: The accurate detection of orthologous segments (also referred to as syntenic segments) plays a key role in comparative genomics, as it is useful for inferring genome rearrangement scenarios and computing whole genome alignments. Although a number of algorithms for detecting orthologous segments have been proposed, none of them contain a framework for optimizing their parameter values.

Methods: In the present study, we propose an algorithm, named OSfinder (Orthologous Segment finder), which uses a novel scoring scheme based on stochastic models. OSfinder takes as input the positions of short homologous regions (also referred to as anchors) and explicitly discriminates orthologous anchors from nonorthologous anchors by using Markov chain models which represent respective geometric distributions of lengths of orthologous and nonorthologous anchors. Such stochastic modeling makes it possible to optimize parameter values by maximizing the likelihood of the input dataset, and to automate the setting of the optimal parameter values.

Results: We validated the accuracies of orthology mapping algorithms on the basis of their consistency with the orthology annotation of genes. Our evaluation tests using mammalian and bacterial genomes demonstrated that OSfinder shows higher accuracy than previous algorithms.

Availability: The OSfinder software was implemented as a C++ program. The software is freely available at http://osfinder.dna.bio.keio.ac.jp under the GNU General Public License.

Contact: hacchy{at}dna.bio.keio.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Prof. Martin Bishop

Received on October 6, 2008; revised on January 28, 2009; accepted on January 29, 2009

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