LocalMotif is a software tool for discovering transcription factor binding motifs in a collection of DNA sequences.  The uniqueness of LocalMotif lies in its ability to discover motifs that occur localized in certain positions in the DNA sequences with respect to a biological landmark.  A well known example is the TATA box motif which usually occurs 25 bp upstream of the transcription start site in eukaryotic systems.

Discovery of localized motifs is important in many contexts, but has become especially relevant in the analysis of high throughput sequencing ChIP-Seq data.  ChIP-Seq can determine thousands of binding sites of a transcription factor (TF) genome-wide with a resolution of ~20bp.  This makes it possible to discover not only the binding motif of the ChIP transcription factor but also the motifs of several other transcription factors that work cooperatively with the ChIP TF.  LocalMotif can effectively discover such co-localized motifs in DNA sequences flanking the ChIP-Seq peaks.

LocalMotif is described in the following paper:

Narang, V., Mittal, A., Sung, W.K. (2009) "Localized motif discovery in gene regulatory sequences", submitted to Bioinformatics.

For correspondance, contact Dr. Wing-Kin Sung at ksung [at] comp.nus.edu.sg