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Nucleic Acids Research 2006 34(Web Server issue):W555-W559; doi:10.1093/nar/gkl224
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Stubb: a program for discovery and analysis of cis-regulatory modules

Saurabh Sinha*, Yupu Liang1 and Eric Siggia1

Department of Computer Science, University of Illinois, Urbana-Champaign NY, USA 1 Center for Studies in Physics and Biology, The Rockefeller University NY, USA

*To whom correspondence should be addressed. Tel: +1 217 333 3233; Fax: +1 217 244 6500; Email: sinhas{at}cs.uiuc.edu

Received February 14, 2006. Revised March 6, 2006. Accepted March 27, 2006.

Given the DNA-binding specificities (motifs) of one or more transcription factors, an important bioinformatics problem is to discover significant clusters of binding sites for the transcription factors(s). Such clusters often correspond to cis-regulatory modules mediating regulation of an adjacent gene. In earlier work, we developed the Stubb program that uses a probabilistic model and a maximum likelihood approach to efficiently detect cis-regulatory modules over genomic scales. It may optionally exploit a second related genome to improve module prediction accuracy. We describe here the use of a web-based interface for the Stubb program. The interface is equipped with a special post-processing step for in-depth analysis of specific modules, in order to reveal individual binding sites predicted in the module. The web server may be accessed at the URL http://stubb.rockefeller.edu/.


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