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

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.

Figure 1

Sequence logo representation of the binding specificity of the transcription factor Elk-1, copied from the Jaspar web site, (identifier MA0028). The height of each column indicates the information content of the corresponding position. The sizes of the characters represent the relative frequency of the corresponding bases.

Figure 2

Representation of the comparison of two weight matrices. The upper, yellow one is a probability matrix taken from the example MEME file (Motif 8 in the example file on the help page). The lower, blue one is the Jaspar count matrix MA0028 for Elk-1. The divergence computed by T-Reg Comparator amounts to 0.644. Thin dashed lines indicate the overlapping part. The frames depict the core consensus GGAA of the ETS family of transcription factors.