A reexamination of information theory-based methods for DNA-binding site identification.

ABSTRACT:

Background

Searching for transcription factor binding sites in genome sequences is still an open problem in bioinformatics. Despite substantial progress, search methods based on information theory remain a standard in the field, even though the full validity of their underlying assumptions has only been tested in artificial settings. Here we use newly available data on transcription factors from different bacterial genomes to make a more thorough assessment of information theory-based search methods.

Results

Our results reveal that conventional benchmarking against artificial sequence data leads frequently to overestimation of search efficiency. In addition, we find that sequence information by itself is often inadequate and therefore must be complemented by other cues, such

SUBMITTER: Erill I 

PROVIDER: S-EPMC2680408 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature