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Bioinformatics Advance Access published online on January 12, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti256
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Bioinformatics © Oxford University Press 2005; all rights reserved.
Received December 6, 2004
Accepted December 28, 2004

Article

Transcription factor binding site identification using the self-organizing map

Shaun Mahony 1*, David Hendrix 2, Aaron Golden 3, Terry J. Smith 1, and Daniel S. Rokhsar 4

1 National Centre for Biomedical Engineering Science, NUI Galway, Galway, Ireland
2 Department of Physics, University of California, Berkeley, CA 94720, USA; Joint Genome Institute, Walnut Creek, CA 94598, USA; Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
3 National Centre for Biomedical Engineering Science, NUI Galway, Galway, Ireland; Department of Information Technology, NUI Galway, Galway, Ireland
4 Joint Genome Institute, Walnut Creek, CA 94598, USA; Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA

* To whom correspondence should be addressed.
Shaun Mahony, E-mail: shaun.mahony{at}nuigalway.ie


  Abstract

Motivation: The automatic identification of over-represented motifs present in a collection of sequences continues to be a challenging problem in computational biology. In this paper, we propose a self-organizing map of position weight matrices as an alternative method for motif discovery. The advantage of this approach is that it can be used to simultaneously characterize every feature present in the data set, thus lessening the chance that weaker signals will be missed. Features identified are ranked in terms of over-representation relative to a background model.

Results: We present an implementation of this approach, named SOMBRERO, which is capable of discovering multiple distinct motifs present in a single data set. Demonstrated here are the advantages of our approach on various data sets and SOMBRERO's improved performance over two popular motif-finding programs; MEME and AlignACE.

Availability: SOMBRERO is available free of charge from http://bioinf.nuigalway.ie/sombrero.


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