title: CLARE: Cracking the LAnguage of Regulatory Elements.
abstract: CLARE is a computational method designed to reveal sequence encryption of tissue-specific regulatory elements. Starting with a set of regulatory elements known to be active in a particular tissue/process, it learns the sequence code of the input set and builds a predictive model from features specific to those elements. The resulting model can then be applied to user-supplied genomic regions to identify novel candidate regulatory elements. CLARE's model also provides a detailed analysis of transcription factors that most likely bind to the elements, making it an invaluable tool for understanding mechanisms of tissue-specific gene regulation.
  
  
  BACKGROUND
  CLARE is freely accessible at http://clare.dcode.org/.
authors.affiliation: Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MA 20894, USA. taherl@ncbi.nlm.nih.gov
authors.forename: Leila
authors.initials: L
authors.lastname: Taher
authors.forename: Leelavati
authors.initials: L
authors.lastname: Narlikar
authors.forename: Ivan
authors.initials: I
authors.lastname: Ovcharenko
mesh_terms: D000818:Animals; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation; D023281:Genomics; D006801:Humans; D051379:Mice; D009928:Organ Specificity; D016548:Prosencephalon / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors