title: Performance evaluation of DNA motif discovery programs.
abstract: Methods for the identification of transcription factor binding sites have proved to be useful for deciphering genetic regulatory networks. The strengths and weaknesses for a number of available web tools are not fully understood. Here, we designed a comprehensive set of performance measures and benchmarked sequence-based motif discovery tools using large scale datasets (derived from Escherichia coli genome and RegulonDB database). The benchmark study showed that nucleotide based and binding site based prediction accuracy is often low and activator binding site based prediction accuracy is high.
authors.affiliation: Department of Computer Sciences, R.S.M.T., U.P. College, Varanasi, India. chand_11_2000@yahoo.com
authors.forename: Chandra Prakash
authors.initials: CP
authors.lastname: Singh
authors.forename: Feroz
authors.initials: F
authors.lastname: Khan
authors.forename: Bhartendu Nath
authors.initials: BN
authors.lastname: Mishra
authors.forename: Durg Singh
authors.initials: DS
authors.lastname: Chauhan