title: FIMO: scanning for occurrences of a given motif.
abstract: A motif is a short DNA or protein sequence that contributes to the biological function of the sequence in which it resides. Over the past several decades, many computational methods have been described for identifying, characterizing and searching with sequence motifs. Critical to nearly any motif-based sequence analysis pipeline is the ability to scan a sequence database for occurrences of a given motif described by a position-specific frequency matrix.
  
  
  RESULTS
  We describe Find Individual Motif Occurrences (FIMO), a software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. The program computes a log-likelihood ratio score for each position in a given sequence database, uses established dynamic programming methods to convert this score to a P-value and then applies false discovery rate analysis to estimate a q-value for each position in the given sequence. FIMO provides output in a variety of formats, including HTML, XML and several Santa Cruz Genome Browser formats. The program is efficient, allowing for the scanning of DNA sequences at a rate of 3.5 Mb/s on a single CPU.
  
  
  METHODS
  FIMO is part of the MEME Suite software toolkit. A web server and source code are available at http://meme.sdsc.edu.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA, USA.
authors.forename: Charles E
authors.initials: CE
authors.lastname: Grant
authors.forename: Timothy L
authors.initials: TL
authors.lastname: Bailey
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
mesh_terms: D020816:Amino Acid Motifs; D001483:Base Sequence; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry*; D030541:Databases, Genetic; D015894:Genome, Human; D006801:Humans; D056510:Position-Specific Scoring Matrices; D012097:Repressor Proteins / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D012097:Repressor Proteins; D004247:DNA