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1: Bioinformatics. 2005 Jun 15;21(12):2909-11. Epub 2005 Apr 6.Click here to read Links

BEST: binding-site estimation suite of tools.

Che D, Jensen S, Cai L, Liu JS.

Department of Computer Science, University of Georgia, Athens, GA 30602, USA. dsche@uga.edu

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@uga.edu, jliu@stat.harvard.edu.

PMID: 15814553 [PubMed - indexed for MEDLINE]