Format

Send to

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2009 Apr 1;25(7):868-74. doi: 10.1093/bioinformatics/btp090. Epub 2009 Feb 17.

M are better than one: an ensemble-based motif finder and its application to regulatory element prediction.

Author information

1
Fred Hutchinson Cancer Research Center, Seattle, WA, USA. cyanover@fhcrc.org

Abstract

MOTIVATION:

Identifying regulatory elements in genomic sequences is a key component in understanding the control of gene expression. Computationally, this problem is often addressed by motif discovery, where the goal is to find a set of mutually similar subsequences within a collection of input sequences. Though motif discovery is widely studied and many approaches to it have been suggested, it remains a challenging and as yet unresolved problem.

RESULTS:

We introduce SAMF (Solution-Aggregating Motif Finder), a novel approach for motif discovery. SAMF is based on a Markov Random Field formulation, and its key idea is to uncover and aggregate multiple statistically significant solutions to the given motif finding problem. In contrast to many earlier methods, SAMF does not require prior estimates on the number of motif instances present in the data, is not limited by motif length, and allows motifs to overlap. Though SAMF is broadly applicable, these features make it particularly well suited for addressing the challenges of prokaryotic regulatory element detection. We test SAMF's ability to find transcription factor binding sites in an Escherichia coli dataset and show that it outperforms previous methods. Additionally, we uncover a number of previously unidentified binding sites in this data, and provide evidence that they correspond to actual regulatory elements.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
19223448
PMCID:
PMC2660878
DOI:
10.1093/bioinformatics/btp090
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center