Assessing computational tools for the discovery of transcription factor binding sites

Tompa, M; Li, N; Bailey, TL; Church, GM; De Moor, Bart; Eskin, E; Favorov, AV; Frith, MC; Fu, YT; Kent, WJ; Makeev, VJ; Mironov, AA; Noble, WS; Pavesi, G; Pesole, G; Regnier, M; Simonis, N; Sinha, S; Thijs, Gert; van Helden, J; Vandenbogaert, M; Weng, ZP; Workman, C; Ye, C; Zhu, Z

doi:10.1038/nbt1053

Assessing computational tools for the discovery of transcription factor binding sites

Author:

Tompa, M

Li, N ; Bailey, TL ; Church, GM ; De Moor, Bart ; Eskin, E ; Favorov, AV ; Frith, MC ; Fu, YT ; Kent, WJ ; Makeev, VJ ; Mironov, AA ; Noble, WS ; Pavesi, G ; Pesole, G ; Regnier, M ; Simonis, N ; Sinha, S ; Thijs, Gert ; van Helden, J ; Vandenbogaert, M ; Weng, ZP ; Workman, C ; Ye, C ; Zhu, Z

Keywords:

genome annotation assessment, regulatory elements, prediction, sequences, genes, dna, SISTA, Science & Technology, Life Sciences & Biomedicine, Biotechnology & Applied Microbiology, GENOME ANNOTATION ASSESSMENT, REGULATORY ELEMENTS, PREDICTION, SEQUENCES, GENES, DNA, Amino Acid Motifs, Animals, Binding Sites, Computational Biology, Databases, Protein, Drosophila, Fungal Proteins, Gene Expression, Humans, Internet, Mice, Reproducibility of Results, Software, Transcription, Genetic

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.