Predicting the binding preference of transcription factors to individual DNA k-mers.

ABSTRACT:

Motivation

Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. Many TF-binding preferences, however, are unknown or poorly characterized, in part due to the difficulty associated with determining their specificity experimentally, and an incomplete understanding of the mechanisms governing sequence specificity. New techniques that estimate the affinity of TFs to all possible k-mers provide a new opportunity to study DNA-protein interaction mechanisms, and may facilitate inference of binding preferences for members of a given TF family when such information is available for other family members.

Results

We employed a new dataset consisting of the relative preferences of mouse homeodomains for all eight-base

SUBMITTER: Alleyne TM 

PROVIDER: S-EPMC2666811 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature