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Bioinformatics Advance Access published online on May 31, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm282
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Tree Gibbs Sampler: Identifying Conserved Motifs without Aligning Orthologous Sequences

Xiaohui Cai 1,2, Haiyan Hu 2 and Xiaoman Shawn Li 1,2,*

1Division of Biostatistics, 2Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, 410 West 10th Street, Indianapolis, IN 46202, USA

*To whom correspondence should be addressed. Xiaoman Shawn Li, E-mail: shawnli{at}iupui.edu


  Abstract

Summary: Tree Gibbs Sampler is a software for identifying motifs by simultaneously using the motif overrepresentation property and the motif evolutionary conservation property. It identifies motifs without depending on pre-aligned orthologous sequences, which makes it useful for the extraction of regulatory elements in multiple genomes of both closely related and distant species.

Availability: The Tree Gibbs Sampler software is freely downloadable at https://compbio.iupui.edu/xiaomanli/LiSoftware/retrieve.php?ID=tgs

Associate Editor: Prof. Alfonso Valencia

Received on January 30, 2007; revised on April 17, 2007; accepted on May 18, 2007

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