Optimized position weight matrices in prediction of novel putative binding sites for transcription factors in the Drosophila melanogaster genome.

ABSTRACT: Position weight matrices (PWMs) have become a tool of choice for the identification of transcription factor binding sites in DNA sequences. DNA-binding proteins often show degeneracy in their binding requirement and thus the overall binding specificity of many proteins is unknown and remains an active area of research. Although existing PWMs are more reliable predictors than consensus string matching, they generally result in a high number of false positive hits. Our previous study introduced a promising approach to PWM refinement in which known motifs are used to computationally mine putative binding sites directly from aligned promoter regions using composition of similar sites. In the present study, we extended this technique originally tested on single examples of transcription factors

SUBMITTER: Morozov VY 

PROVIDER: S-EPMC3735551 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature