title: BEST: binding-site estimation suite of tools.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  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.
authors.affiliation: Department of Computer Science, University of Georgia, Athens, GA 30602, USA. dsche@uga.edu
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Che
authors.forename: Shane
authors.initials: S
authors.lastname: Jensen
authors.forename: Liming
authors.initials: L
authors.lastname: Cai
authors.forename: Jun S
authors.initials: JS
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003196:Computer Graphics; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors; D004247:DNA