DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.

ABSTRACT:

Motivation

Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs, etc. Several methods have been developed to jointly account for DNA sequence and shape properties in predicting TF binding affinity. However, a limitation of these methods is that they typically require a training set of aligned TF binding sites.

Results

We describe a sequence + shape kernel that leverages DNA sequence and shape information to better understand protein-DNA binding preference and affinity. This kernel extends an existing class of k-mer based sequence kernels, based on the recently described di-

SUBMITTER: Ma W 

PROVIDER: S-EPMC5870879 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature