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

/2002/3/3/research/0013.1 Research Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA Esperanza Benítez-Bellón, Gabriel Moreno-Hagelsieb and Julio Collado-Vides Address: Program of Computational Genomics, CIFN, UNAM, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico. Correspondence: Gabriel Moreno-Hagelsieb. E-mail: moreno@cifn.unam.mx. Julio Collado-Vides. E-mail: collado@cifn.unam.mx Published: 21 February 2002 Received: 16 August 2001 Revised: 20 November 2001 Accepted: 28 January 2002 Genome Biology 2002, 3(3):research0013.1–0013.16 The electronic version of this article is the complete one and can be found online at /2002/3/3/research/0013 ? 2002 Benítez-Bellón et al., licensee BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) 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. Detailed evaluation also helps to improve and understand the behavior of the different methods and computational strategies. Results: We used a collection of 86 regulons from Escherichia coli as datasets to evaluate two methods for pattern discovery and pattern sea