PMID- 21330290
OWN - NLM
STAT- MEDLINE
DCOM- 20110829
LR  - 20240104
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Print)
IS  - 1367-4803 (Linking)
VI  - 27
IP  - 7
DP  - 2011 Apr 1
TI  - FIMO: scanning for occurrences of a given motif.
PG  - 1017-8
LID - 10.1093/bioinformatics/btr064 [doi]
AB  - 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. AVAILABILITY AND IMPLEMENTATION: 
      FIMO is part of the MEME Suite software toolkit. A web server and source code are 
      available at http://meme.sdsc.edu.
FAU - Grant, Charles E
AU  - Grant CE
AD  - Department of Genome Sciences, University of Washington, Seattle, WA, USA.
FAU - Bailey, Timothy L
AU  - Bailey TL
FAU - Noble, William Stafford
AU  - Noble WS
LA  - eng
GR  - R01 RR021692/RR/NCRR NIH HHS/United States
GR  - 2 R01 RR021692/RR/NCRR NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20110216
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
RN  - 0 (CCCTC-Binding Factor)
RN  - 0 (CTCF protein, human)
RN  - 0 (Repressor Proteins)
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - *Amino Acid Motifs
MH  - Base Sequence
MH  - Binding Sites
MH  - CCCTC-Binding Factor
MH  - Conserved Sequence
MH  - DNA/*chemistry
MH  - Databases, Genetic
MH  - Genome, Human
MH  - Humans
MH  - Position-Specific Scoring Matrices
MH  - Repressor Proteins/metabolism
MH  - Sequence Analysis, DNA/*methods
MH  - Sequence Analysis, Protein/*methods
MH  - *Software
PMC - PMC3065696
EDAT- 2011/02/19 06:00
MHDA- 2011/08/30 06:00
PMCR- 2011/02/16
CRDT- 2011/02/19 06:00
PHST- 2011/02/19 06:00 [entrez]
PHST- 2011/02/19 06:00 [pubmed]
PHST- 2011/08/30 06:00 [medline]
PHST- 2011/02/16 00:00 [pmc-release]
AID - btr064 [pii]
AID - 10.1093/bioinformatics/btr064 [doi]
PST - ppublish
SO  - Bioinformatics. 2011 Apr 1;27(7):1017-8. doi: 10.1093/bioinformatics/btr064. Epub 
      2011 Feb 16.