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Nucleic Acids Research 2005 33(Web Server Issue):W438-W441; doi:10.1093/nar/gki590
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© The Author 2005. 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{at}oupjournals.org

Article

T-Reg Comparator: an analysis tool for the comparison of position weight matrices

Stefan Roepcke*, Steffen Grossmann, Sven Rahmann1 and Martin Vingron

Max Planck Institute for Molecular Genetics Ihnestrasse 73, 14195 Berlin, Germany 1Department of Genome Informatics, University of Bielefeld 33594 Bielefeld, Germany

*To whom correspondence should be addressed. Tel: +49 30 84131159; Fax: +49 30 84131152; Email: roepcke{at}molgen.mpg.de

Received February 14, 2005. Revised April 19, 2005. Accepted May 3, 2005.

T-Reg Comparator is a novel software tool designed to support research into transcriptional regulation. Sequence motifs representing transcription factor binding sites are usually encoded as position weight matrices. The user inputs a set of such weight matrices or binding site sequences and our program matches them against the T-Reg database, which is presently built on data from the Transfac [E. Wingender (2004) In Silico Biol., 4, 55–61] and Jaspar [A. Sandelin, W. Alkema, P. Engstrom, W. W. Wasserman and B. Lenhard (2004) Nucleic Acids Res., 32, D91–D94]. Our tool delivers a detailed report on similarities between user-supplied motifs and motifs in the database. Apart from simple one-to-one relationships, T-Reg Comparator is also able to detect similarities between submatrices. In addition, we provide a user interface to a program for sequence scanning with weight matrices. Typical areas of application for T-Reg Comparator are motif and regulatory module finding and annotation of regulatory genomic regions. T-Reg Comparator is available at http://treg.molgen.mpg.de.


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