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Bioinformatics Advance Access originally published online on January 12, 2005
Bioinformatics 2005 21(9):1807-1814; doi:10.1093/bioinformatics/bti256
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Transcription factor binding site identification using the self-organizing map

Shaun Mahony 1,*, David Hendrix 3,4,5, Aaron Golden 1,2, Terry J. Smith 1 and Daniel S. Rokhsar 4,5

1National Centre for Biomedical Engineering Science, NUI Galway Galway, Ireland
2Department of Information Technology, NUI Galway Galway, Ireland
3Department of Physics, University of California Berkeley, CA 94720, USA
4Center for Integrative Genomics, University of California Berkeley, CA 94720, USA
5Joint Genome Institute Walnut Creek, CA 94598, USA

*To whom correspondence should be addressed.

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 dataset, 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 (self-organizing map for biological regulatory element recognition and ordering), which is capable of discovering multiple distinct motifs present in a single dataset. Demonstrated here are the advantages of our approach on various datasets 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

Contact: shaun.mahony{at}nuigalway.ie

Supplementary information: http://bioinf.nuigalway.ie/sombrero/additional


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