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Nucleic Acids Research Advance Access published online on May 5, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm265
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© 2007 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.

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The Gibbs Centroid Sampler

William A. Thompson1,*, Lee A. Newberg2,3, Sean Conlan4, Lee Ann McCue5 and Charles E. Lawrence1

1Center for Computational Molecular Biology and the Division of Applied Mathematics, Brown University, Providence, RI 02912, USA, 2The Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA, 3Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA, 4Columbia University, New York, NY 10032, USA and 5Pacific Northwest National Laboratory, Richland, WA 99352, USA

*To whom correspondence should be addressed: Tel: +1-401-863-2048; Email: william_thompson_l{at}brown.edu

Received January 31, 2007. Revised March 27, 2007. Accepted April 8, 2007.

The Gibbs Centroid Sampler is a software package designed for locating conserved elements in biopolymer sequences. The Gibbs Centroid Sampler reports a centroid alignment, i.e. an alignment that has the minimum total distance to the set of samples chosen from the a posteriori probability distribution of transcription factor binding-site alignments. In so doing, it garners information from the full ensemble of solutions, rather than only the single most probable point that is the target of many motif-finding algorithms, including its predecessor, the Gibbs Recursive Sampler. Centroid estimators have been shown to yield substantial improvements, in both sensitivity and positive predictive values, to the prediction of RNA secondary structure and motif finding. The Gibbs Centroid Sampler, along with interactive tutorials, an online user manual, and information on downloading the software, is available at: http://bayesweb.wadsworth.org/gibbs/gibbs.html.


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