title: Finding motifs in the twilight zone.
abstract: BACKGROUND
  Gene activity is often affected by binding transcription factors to short fragments in DNA sequences called motifs. Identification of subtle regulatory motifs in a DNA sequence is a difficult pattern recognition problem. In this paper we design a new motif finding algorithm that can detect very subtle motifs.
  
  
  RESULTS
  We introduce the notion of a multiprofile and use it for finding subtle motifs in DNA sequences. Multiprofiles generalize the notion of a profile and allow one to detect subtle patterns that escape detection by the standard profiles. Our MULTIPROFILER algorithm outperforms other leading motif finding algorithms in a number of synthetic models. Moreover, it can be shown that in some previously studied motif models, MULTIPROFILER is capable of pushing the performance envelope to its theoretical limits.
  
  
  BACKGROUND
  http://www-cse.ucsd.edu/groups/bioinformatics/software.html
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA. keich@cs.ucsd.edu
authors.forename: U
authors.initials: U
authors.lastname: Keich
authors.forename: P A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs / Q000235:genetics*; D001483:Base Sequence; D019985:Benchmarking; D016384:Consensus Sequence / Q000235:genetics; D004247:DNA / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics; D011786:Quality Control; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA