Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2011 Apr 1;27(7):1017-8. doi: 10.1093/bioinformatics/btr064. Epub 2011 Feb 16.

FIMO: scanning for occurrences of a given motif.

Author information

  • 1Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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.

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.

PMID:
21330290
[PubMed - indexed for MEDLINE]
PMCID:
PMC3065696
Free PMC Article

Images from this publication.See all images (1)Free text

Fig. 1.
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Write to the Help Desk