The value of position-specific priors in motif discovery using MEME.

ABSTRACT:

Background

Position-specific priors have been shown to be a flexible and elegant way to extend the power of Gibbs sampler-based motif discovery algorithms. Information of many types-including sequence conservation, nucleosome positioning, and negative examples-can be converted into a prior over the location of motif sites, which then guides the sequence motif discovery algorithm. This approach has been shown to confer many of the benefits of conservation-based and discriminative motif discovery approaches on Gibbs sampler-based motif discovery methods, but has not previously been studied with methods based on expectation maximization (EM).

Results

We extend the popular EM-based MEME algorithm to utilize position-specific priors and demonstrate their effectiveness for discove

SUBMITTER: Bailey TL 

PROVIDER: S-EPMC2868008 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature