Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA.

ABSTRACT:

Background

Sites in DNA that bind regulatory proteins can be detected computationally in various ways. Pattern discovery methods analyze collections of genes suspected to be co-regulated on the evidence, for example, of clustering of transcriptome data. Pattern searching methods use sequences with known binding sites to find other genes regulated by a given protein. Such computational methods are important strategies in the discovery and elaboration of regulatory networks and can provide the experimental biologist with a precise prediction of a binding site or identify a gene as a member of a set of co-regulated genes (a regulon). As more variations on such methods are published, however, thorough evaluation is necessary, as performance may differ depending on the conditions of use

SUBMITTER: Benitez-Bellon E 

PROVIDER: S-EPMC88811 | biostudies-literature | 2002

REPOSITORIES: biostudies-literature