MProfiler: A Profile-Based Method for DNA Motif Discovery
PRIB '09 Proceedings of the 4th IAPR International Conference on Pattern Recognition in Bioinformatics
PFP: a computational framework for phylogenetic footprinting in prokaryotic genomes
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
ISCIS'06 Proceedings of the 21st international conference on Computer and Information Sciences
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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