Assessing computational tools for the discovery of transcription factor binding sites.
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.
Tompa
Martin
M
Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195-2350, USA. tompa@cs.washington.edu
Li
Nan
N
Bailey
Timothy L
TL
Church
George M
GM
De Moor
Bart
B
Eskin
Eleazar
E
Favorov
Alexander V
AV
Frith
Martin C
MC
Fu
Yutao
Y
Kent
W James
WJ
Makeev
Vsevolod J
VJ
Mironov
Andrei A
AA
Noble
William Stafford
WS
Pavesi
Giulio
G
Pesole
Graziano
G
Régnier
Mireille
M
Simonis
Nicolas
N
Sinha
Saurabh
S
Thijs
Gert
G
van Helden
Jacques
J
Vandenbogaert
Mathias
M
Weng
Zhiping
Z
Workman
Christopher
C
Ye
Chun
C
Zhu
Zhou
Z
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
D005656:Fungal Proteins