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Journal Article

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

MPS-Authors

Roepcke,  Stefan
Max Planck Society;

Grossmann,  Steffen
Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons50480

Rahmann,  Sven
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons50613

Vingron,  Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Fulltext (public)

W438.pdf
(Any fulltext), 74KB

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Citation

Roepcke, S., Grossmann, S., Rahmann, S., & Vingron, M. (2005). T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Web Server Issue, W438-W341. doi:10.1093/nar/gki590.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0010-8658-C
Abstract
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.