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Bioinformatics Advance Access originally published online on November 10, 2006
Bioinformatics 2007 23(2):243-244; doi:10.1093/bioinformatics/btl568
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PEAKS: identification of regulatory motifs by their position in DNA sequences

Nicolás Bellora 1, Domènec Farré 2 and M. Mar Albà 1,3,*

1 Research Unit on Biomedical Informatics, Universitat Pompeu Fabra Barcelona 08003, Spain
2 Centre for Genomic Regulation Barcelona 08003, Spain
3 Catalan Institution for Research and Advanced Studies—Municipal Institute of Medical Research Barcelona 08003, Spain

*To whom correspondence should be addressed.


  Abstract

Summary: Many DNA functional motifs tend to accumulate or cluster at specific gene locations. These locations can be detected, in a group of gene sequences, as high frequency ‘peaks’ with respect to a reference position, such as the transcription start site (TSS). We have developed a web tool for the identification of regions containing significant motif peaks. We show, by using different yeast gene datasets, that peak regions are strongly enriched in experimentally-validated motifs and contain potentially important novel motifs.

Availability: http://genomics.imim.es/peaks

Contact: malba{at}imim.es

Supplementary information: Supplementary Data are available at Bioinformatics online.

Associate Editor: David Rocke

Received on July 4, 2006; revised on October 18, 2006; accepted on November 5, 2006

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