Theoretical and empirical quality assessment of transcription factor-binding motifs.

ABSTRACT: Position-specific scoring matrices (PSSMs) are routinely used to predict transcription factor (TF)-binding sites in genome sequences. However, their reliability to predict novel binding sites can be far from optimum, due to the use of a small number of training sites or the inappropriate choice of parameters when building the matrix or when scanning sequences with it. Measures of matrix quality such as E-value and information content rely on theoretical models, and may fail in the context of full genome sequences. We propose a method, implemented in the program 'matrix-quality', that combines theoretical and empirical score distributions to assess reliability of PSSMs for predicting TF-binding sites. We applied 'matrix-quality' to estimate the predictive capacity of matrices for bacterial,

SUBMITTER: Medina-Rivera A 

PROVIDER: S-EPMC3035439 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature