DECOD: fast and accurate discriminative DNA motif finding.

ABSTRACT:

Motivation

Motif discovery is now routinely used in high-throughput studies including large-scale sequencing and proteomics. These datasets present new challenges. The first is speed. Many motif discovery methods do not scale well to large datasets. Another issue is identifying discriminative rather than generative motifs. Such discriminative motifs are important for identifying co-factors and for explaining changes in behavior between different conditions.

Results

To address these issues we developed a method for DECOnvolved Discriminative motif discovery (DECOD). DECOD uses a k-mer count table and so its running time is independent of the size of the input set. By deconvolving the k-mers DECOD considers context information without using the sequences directly. DECOD outper

SUBMITTER: Huggins P 

PROVIDER: S-EPMC3157928 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature