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

By Trevis M. Alleyne, Lourdes Peña-Castillo, Gwenael Badis, Shaheynoor Talukder, Michael F. Berger, Andrew R. Gehrke, Anthony A. Philippakis, Martha L. Bulyk, Quaid D. Morris and Timothy R. Hughes

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

Topics: Original Papers
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:2666811
Provided by: PubMed Central
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