Analysis abstract


Nature Biotechnology 23, 137 - 144 (2005)
Published online: 6 January 2005 | doi:10.1038/nbt1053

Assessing computational tools for the discovery of transcription factor binding sites

Martin Tompa1,2, Nan Li1, Timothy L Bailey3, George M Church4, Bart De Moor5, Eleazar Eskin6, Alexander V Favorov7,8, Martin C Frith9, Yutao Fu9, W James Kent10, Vsevolod J Makeev7,8, Andrei A Mironov7,11, William Stafford Noble1,2, Giulio Pavesi12, Graziano Pesole13, Mireille Régnier14, Nicolas Simonis15, Saurabh Sinha16, Gert Thijs5, Jacques van Helden15, Mathias Vandenbogaert14, Zhiping Weng9, Christopher Workman17, Chun Ye18 & Zhou Zhu4


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.

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  1. Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195-2350, USA.
  2. Department of Genome Sciences, Box 357730, University of Washington, Seattle, Washington 98195-7730, USA.
  3. Institute for Molecular Biosciences, University of Queensland, Brisbane, Australia.
  4. Department of Genetics and Lipper Center for Computational Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
  5. ESAT-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium.
  6. Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA.
  7. State Scientific Centre 'GosNIIGenetica,' 1st Dorozhny pr. 1, Moscow, 117545, Russia.
  8. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia.
  9. Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA.
  10. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA.
  11. Department of Bioengineering and Bioinformatics, Moscow State University, Lab. Bldg B, Vorobiovy Gory 1-33, Moscow 119992, Russia.
  12. Department of Computer Science and Communication (D.I.Co), University of Milan, Milan, Italy.
  13. Department of Biomolecular Science and Biotechnology, University of Milan, Milan, Italy.
  14. INRIA Rocquencourt, Domaine de Voluceau B.P. 105, 78153 Le Chesnay, France.
  15. SCMB-Université Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, 1050 Bruxelles, Belgium.
  16. Center for Studies in Physics and Biology, The Rockefeller University, New York, New York 10021, USA.
  17. Department of Bioengineering, University of California, San Diego, California 92093, USA.
  18. Bioinformatics Program, University of California, San Diego, California 92093, USA.

Correspondence to: Martin Tompa1,2 e-mail: tompa@cs.washington.edu



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