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Bioinformatics Advance Access published online on November 10, 2006
Bioinformatics, 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
Received July 4, 2006
Revised October 18, 2006
Accepted November 5, 2006

Applications note

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

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

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

* To whom correspondence should be addressed.
M. Mar Albà, E-mail: malba{at}imim.es


  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. 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.

Supplementary Material: Figure S1 and Table S1.

Associate Editor: David Rocke
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