Dinucleotide weight matrices for predicting transcription factor binding sites: generalizing the position weight matrix.

ABSTRACT:

Background

Identifying transcription factor binding sites (TFBS) in silico is key in understanding gene regulation. TFBS are string patterns that exhibit some variability, commonly modelled as "position weight matrices" (PWMs). Though convenient, the PWM has significant limitations, in particular the assumed independence of positions within the binding motif; and predictions based on PWMs are usually not very specific to known functional sites. Analysis here on binding sites in yeast suggests that correlation of dinucleotides is not limited to near-neighbours, but can extend over considerable gaps.

Methodology/principal findings

I describe a straightforward generalization of the PWM model, that considers frequencies of dinucleotides instead of individual nucleotides. Unlike

SUBMITTER: Siddharthan R 

PROVIDER: S-EPMC2842295 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature