T-Reg Comparator: an analysis tool for the comparison of position weight matrices.
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.
Roepcke
Stefan
S
Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany. roepcke@molgen.mpg.de
Grossmann
Steffen
S
Rahmann
Sven
S
Vingron
Martin
M
D001665:Binding Sites; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods*; D020407:Internet; D012045:Regulatory Sequences, Nucleic Acid; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
D014157:Transcription Factors