Assessing computational tools for the discovery of transcription factor binding sites

Assessing computational tools for the discovery of transcription factor binding sites. Tompa, M., Li, N., Bailey, T. L, Church, G. M, Moor, B. D., Eskin, E., Favorov, A. V, Frith, M. C, Fu, Y., Kent, W. J., Makeev, V. J, Mironov, A. A, Noble, W. S., Pavesi, G., Pesole, G., Régnier, M., Simonis, N., Sinha, S., Thijs, G., van Helden, J., Vandenbogaert, M., Weng, Z., Workman, C., Ye, C., & Zhu, Z. Nat Biotechnol, 23(1):137–144, 2005.
doi abstract bibtex

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.

@Article{tompa05assessing,
  author    = {Martin Tompa and Nan Li and Timothy L Bailey and George M Church and Bart De Moor and Eleazar Eskin and Alexander V Favorov and Martin C Frith and Yutao Fu and W. James Kent and Vsevolod J Makeev and Andrei A Mironov and William Stafford Noble and Giulio Pavesi and Graziano Pesole and Mireille R{\'e}gnier and Nicolas Simonis and Saurabh Sinha and Gert Thijs and Jacques van Helden and Mathias Vandenbogaert and Zhiping Weng and Christopher Workman and Chun Ye and Zhou Zhu},
  title     = {Assessing computational tools for the discovery of transcription factor binding sites},
  journal   = {Nat Biotechnol},
  year      = {2005},
  volume    = {23},
  number    = {1},
  pages     = {137--144},
  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.},
  doi       = {10.1038/nbt1053},
  file      = {TompaEtAl_AssessingComputationalToolsTranscriptionFactorBinding_NatBiotechnol_2005.pdf:2005/TompaEtAl_AssessingComputationalToolsTranscriptionFactorBinding_NatBiotechnol_2005.pdf:PDF},
  keywords  = {motif finding, implanted motif},
  owner     = {Sebastian},
  pmid      = {15637633},
  timestamp = {2006.04.04},
}

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