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Nucleic Acids Research, 2003, Vol. 31, No. 13 3580-3585
© 2003 Oxford University Press

Gibbs Recursive Sampler: finding transcription factor binding sites

William Thompson1, Eric C. Rouchka2 and Charles E. Lawrence1,3

1 The Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA 2 Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA 3 Computer Science Department, Rensselaer Polytechnic Institute, Troy, NY 12180, USA

*To whom correspondence should be addressed. Tel: +1 5184867882; Fax: +1 518 473 2900; Email: thompson{at}wadsworth.org

The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs Recursive Sampler, which has been developed specifically for locating multiple transcription factor binding sites for multiple transcription factors simultaneously in unaligned DNA sequences that may be heterogeneous in DNA composition. Here we describe the basic operation of the web-based version of this sampler. The sampler may be acces-sed at http://bayesweb.wadsworth.org/gibbs/gibbs.html and at http://www.bioinfo.rpi.edu/applications/bayesian/gibbs/gibbs.html. An online user guide is available at http://bayesweb.wadsworth.org/gibbs/bernoulli.html and at http://www.bioinfo.rpi.edu/applications/bayesian/gibbs/manual/bernoulli.html. Solaris, Solaris.x86 and Linux versions of the sampler are available as stand-alone programs for academic and not-for-profit users. Commercial licenses are also available. The Gibbs Recursive Sampler is distributed in accordance with the ISCB level 0 guidelines and a requirement for citation of use in scientific publications.


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