title: ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites.
abstract: BACKGROUND
  The prediction and annotation of the genomic regions involved in gene expression has been largely explored. Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding sites (TFBSs) largely unexplored and with important quantitative and qualitative methodological gaps.
  
  
  RESULTS
  We have developed ReLA (for REgulatory region Local Alignment tool), a unique tool optimized with the Smith-Waterman algorithm that allows local searches of conserved TFBS clusters and the detection of regulatory regions proximal to genes and enhancer regions. ReLA's performance shows specificities of 81 and 50% when tested on experimentally validated proximal regulatory regions and enhancers, respectively.
authors.affiliation: Joint IRB-BSC program on Computational Biology, BSC c/ Jordi Girona 29, Catalonia.
authors.forename: Santi
authors.initials: S
authors.lastname: González
authors.forename: Bàrbara
authors.initials: B
authors.lastname: Montserrat-Sentís
authors.forename: Friman
authors.initials: F
authors.lastname: Sánchez
authors.forename: Montserrat
authors.initials: M
authors.lastname: Puiggròs
authors.forename: Enrique
authors.initials: E
authors.lastname: Blanco
authors.forename: Alex
authors.initials: A
authors.lastname: Ramirez
authors.forename: David
authors.initials: D
authors.lastname: Torrents
mesh_terms: D000465:Algorithms; D000818:Animals; D006801:Humans; D011485:Protein Binding; D012045:Regulatory Sequences, Nucleic Acid; D057386:Search Engine; D016415:Sequence Alignment / Q000379:methods*; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*; D024363:Transcription Initiation Site
chemical_list: D014157:Transcription Factors