DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices.

ABSTRACT:

Background

The accurate determination of transcription factor binding affinities is an important problem in biology and key to understanding the gene regulation process. Position weight matrices are commonly used to represent the binding properties of transcription factor binding sites but suffer from low information content and a large number of false matches in the genome. We describe a novel algorithm for the refinement of position weight matrices representing transcription factor binding sites based on experimental data, including ChIP-chip analyses. We present an iterative weight matrix optimization method that is more accurate in distinguishing true transcription factor binding sites from a negative control set. The initial position weight matrix comes from JASPAR, TRANSFAC o

SUBMITTER: da Piedade I 

PROVIDER: S-EPMC2788558 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature