FIMO: Scanning for occurrences of a given motif

Grant, Charles E., Bailey, Timothy L. and Noble, William S. (2011) FIMO: Scanning for occurrences of a given motif. Bioinformatics, 27 12: 1017-1018. doi:10.1093/bioinformatics/btr064


Author Grant, Charles E.
Bailey, Timothy L.
Noble, William S.
Title FIMO: Scanning for occurrences of a given motif
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1367-4803
1367-4811
Publication date 2011-04-01
Sub-type Article (original research)
DOI 10.1093/bioinformatics/btr064
Open Access Status Not yet assessed
Volume 27
Issue 12
Start page 1017
End page 1018
Total pages 2
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Subject 1303 Biochemistry
1312 Molecular Biology
1703 Computational Theory and Mathematics
1706 Computer Science Applications
2605 Computational Mathematics
2613 Statistics and Probability
2700 Medicine
Abstract Summary: 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.
Formatted abstract
Summary: 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.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2012 Collection
School of Chemistry and Molecular Biosciences
Institute for Molecular Bioscience - Publications
 
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Created: Tue, 25 Oct 2011, 03:55:56 EST by Dr Timothy Bailey on behalf of School of Chemistry & Molecular Biosciences