Improved predictions of transcription factor binding sites using physicochemical features of DNA.

ABSTRACT: Typical approaches for predicting transcription factor binding sites (TFBSs) involve use of a position-specific weight matrix (PWM) to statistically characterize the sequences of the known sites. Recently, an alternative physicochemical approach, called SiteSleuth, was proposed. In this approach, a linear support vector machine (SVM) classifier is trained to distinguish TFBSs from background sequences based on local chemical and structural features of DNA. SiteSleuth appears to generally perform better than PWM-based methods. Here, we improve the SiteSleuth approach by considering both new physicochemical features and algorithmic modifications. New features are derived from Gibbs energies of amino acid-DNA interactions and hydroxyl radical cleavage profiles of DNA. Algorithmic modification

SUBMITTER: Maienschein-Cline M 

PROVIDER: S-EPMC3526315 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature