title: Assessing computational tools for the discovery of transcription factor binding sites.
abstract: The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available for this task. The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.
authors.affiliation: Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195-2350, USA. tompa@cs.washington.edu
authors.forename: Martin
authors.initials: M
authors.lastname: Tompa
authors.forename: Nan
authors.initials: N
authors.lastname: Li
authors.forename: Timothy L
authors.initials: TL
authors.lastname: Bailey
authors.forename: George M
authors.initials: GM
authors.lastname: Church
authors.forename: Bart
authors.initials: B
authors.lastname: De Moor
authors.forename: Eleazar
authors.initials: E
authors.lastname: Eskin
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Favorov
authors.forename: Martin C
authors.initials: MC
authors.lastname: Frith
authors.forename: Yutao
authors.initials: Y
authors.lastname: Fu
authors.forename: W James
authors.initials: WJ
authors.lastname: Kent
authors.forename: Vsevolod J
authors.initials: VJ
authors.lastname: Makeev
authors.forename: Andrei A
authors.initials: AA
authors.lastname: Mironov
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
authors.forename: Giulio
authors.initials: G
authors.lastname: Pavesi
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
authors.forename: Mireille
authors.initials: M
authors.lastname: Régnier
authors.forename: Nicolas
authors.initials: N
authors.lastname: Simonis
authors.forename: Saurabh
authors.initials: S
authors.lastname: Sinha
authors.forename: Gert
authors.initials: G
authors.lastname: Thijs
authors.forename: Jacques
authors.initials: J
authors.lastname: van Helden
authors.forename: Mathias
authors.initials: M
authors.lastname: Vandenbogaert
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
authors.forename: Christopher
authors.initials: C
authors.lastname: Workman
authors.forename: Chun
authors.initials: C
authors.lastname: Ye
authors.forename: Zhou
authors.initials: Z
authors.lastname: Zhu
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D004330:Drosophila; D005656:Fungal Proteins / Q000737:chemistry; D015870:Gene Expression; D006801:Humans; D020407:Internet; D051379:Mice; D015203:Reproducibility of Results; D012984:Software; D014158:Transcription, Genetic
chemical_list: D005656:Fungal Proteins