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Bioinformatics Advance Access published online on April 6, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti425
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 14, 2004
Revised March 24, 2005
Accepted March 31, 2005

Applications note

BEST: Binding-site Estimation Suite of Tools

Dongsheng Che 1*, Shane Jensen 2, Liming Cai 1, and Jun S. Liu 3

1 Department of Computer Science, University of Georgia, Athens, GA 30602
2 Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA 19102
3 Department of Statistics, Harvard University, Cambridge, MA 02138-2931

* To whom correspondence should be addressed.
Dongsheng Che, E-mail: dsche{at}uga.edu


  Abstract

Summary: The purpose of our Binding-site Estimation Suite of Tools (BEST) is two-fold: to provide a platform for using and comparing different motif-finding programs for transcription factor binding site prediction, and to improve the accuracy of these predictions by further optimization. Our software package BEST includes four commonly-used motif-finding programs: AlignACE, BioProspector, CONSENSUS, and MEME, as well as the optimization program BioOptimizer. BEST allows the user to run programs either separately or sequentially, and manages all programs by automating the common inputs and the optimization procedure. The BEST system was implemented in Qt, a C++ application development framework, and was compiled and executed on Linux operating systems.

Availability: BEST is available for download at http://www.cs.uga.edu/~che/BEST and http://www.fas.harvard.edu/~junliu/BEST.


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