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Bioinformatics Advance Access originally published online on April 6, 2005
Bioinformatics 2005 21(12):2909-2911; 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{at}oupjournals.org

BEST: Binding-site Estimation Suite of Tools

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

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

*To whom correspondence should be addressed.

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

Contact: dsche{at}uga.edu, jliu{at}stat.harvard.edu


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