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.