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Bioinformatics Advance Access originally published online on April 13, 2006
Bioinformatics 2006 22(18):2310-2312; doi:10.1093/bioinformatics/btl125
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures

Rajesh Chowdhary 1, Sin Lam Tan 1, R. Ayesha Ali 2, Brent Boerlage 3, Limsoon Wong 4 and Vladimir B Bajic 1,5,*

1 Knowledge Extraction Lab, Institute for Infocomm Research 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
2 Department of Mathematics and Statistics, University of Guelph Guelph ON, Canada N1G 2W1, Canada
3 Norsys Software Corporation, 3512 West 23rd Avenue Vancouver, BC, Canada V6S 1K5, Canada
4 School of Computing, National University of Singapore Singapore 117543, Singapore
5 University of the Western Cape, South African National Bioinformatics Institute (SANBI) Private Bag X17, Bellville 7535, South Africa

*To whom correspondence should be addressed.

Summary: Dragon Promoter Mapper (DPM) is a tool to model promoter structure of co-regulated genes using methodology of Bayesian networks. DPM exploits an exhaustive set of motif features (such as motif, its strand, the order of motif occurrence and mutual distance between the adjacent motifs) and generates models from the target promoter sequences, which may be used to (1) detect regions in a genomic sequence which are similar to the target promoters or (2) to classify other promoters as similar or not to the target promoter group. DPM can also be used for modelling of enhancers and silencers.

Availability: http://defiant.i2r.a-star.edu.sg/projects/BayesPromoter/

Contact: vlad{at}sanbi.ac.za

Supplementary information: Manual for using DPM web server is provided at http://defiant.i2r.a-star.edu.sg/projects/BayesPromoter/html/manual/manual.htm

Received on December 29, 2005; revised on March 26, 2006; accepted on March 28, 2006

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