title: Scoring functions for transcription factor binding site prediction.
abstract: BACKGROUND
  Transcription factor binding site (TFBS) prediction is a difficult problem, which requires a good scoring function to discriminate between real binding sites and background noise. Many scoring functions have been proposed in the literature, but it is difficult to assess their relative performance, because they are implemented in different software tools using different search methods and different TFBS representations.
  
  
  RESULTS
  Here we compare how several scoring functions perform on both real and semi-simulated data sets in a common test environment. We have also developed two new scoring functions and included them in the comparison. The data sets are from the yeast (S. cerevisiae) genome. Our new scoring function LLBG (least likely under the background model) performs best in this study. It achieves the best average rank for the correct motifs. Scoring functions based on positional bias performed quite poorly in this study.
  
  
  CONCLUSIONS
  LLBG may provide an interesting alternative to current scoring functions for TFBS prediction.
authors.affiliation: Institute of Computational Science, ETH, 8092 Zurich, Switzerland. friberg@inf.ethz.ch
authors.forename: Markus
authors.initials: M
authors.lastname: Friberg
authors.forename: Peter
authors.initials: P
authors.lastname: von Rohr
authors.forename: Gaston
authors.initials: G
authors.lastname: Gonnet
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D019277:Entropy; D005656:Fungal Proteins / Q000737:chemistry; D008024:Ligands; D015233:Models, Statistical; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae; D016415:Sequence Alignment; D012984:Software; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics*
chemical_list: D005656:Fungal Proteins; D008024:Ligands; D011506:Proteins; D014157:Transcription Factors; D004247:DNA