Comparison of discriminative motif optimization using matrix and DNA shape-based models.

ABSTRACT:

Background

Transcription factor (TF) binding site specificity is commonly represented by some form of matrix model in which the positions in the binding site are assumed to contribute independently to the site's activity. The independence assumption is known to be an approximation, often a good one but sometimes poor. Alternative approaches have been developed that use k-mers (DNA "words" of length k) to account for the non-independence, and more recently DNA structural parameters have been incorporated into the models. ChIP-seq data are often used to assess the discriminatory power of motifs and to compare different models. However, to measure the improvement due to using more complex models, one must compare to optimized matrix models.

Results

We describe a program "Discri

SUBMITTER: Ruan S 

PROVIDER: S-EPMC5840810 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature