Assessing computational tools for the discovery of transcription factor binding sites

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

Nat Biotechnol, Vol. 23, No. 1. (2005), pp. 137-44.

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algorithms, binding-site-prediction, evaluation

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.

@article{MR:Tom2005, 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.}, author = {Tompa, M. and Li, N. and Bailey, T. L. and Church, G. M. and De Moor, B. and Eskin, E. and Favorov, A. V. and Frith, M. C. and Fu, Y. and Kent, W. J. and Makeev, V. J. and Mironov, A. A. and Noble, W. S. and Pavesi, G. and Pesole, G. and Regnier, M. and Simonis, N. and Sinha, S. and Thijs, G. and van Helden, J. and Vandenbogaert, M. and Weng, Z. and Workman, C. and Ye, C. and Zhu, Z. }, citeulike-article-id = {1746497}, journal = {Nat Biotechnol}, keywords = {algorithms, binding-site-prediction, evaluation}, number = {1}, pages = {137--44}, posted-at = {2007-10-11 23:24:48}, priority = {0}, title = {Assessing computational tools for the discovery of transcription factor binding sites}, volume = {23}, year = {2005} }

RIS record

TY - JOUR ID - MR:Tom2005 L3 - citeulike-article-id:1746497 TI - Assessing computational tools for the discovery of transcription factor binding sites JF - Nat Biotechnol VL - 23 IS - 1 SP - 137 EP - 44 N2 - 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. KW - algorithms KW - binding-site-prediction KW - evaluation AU - Tompa, M AU - Li, N AU - Bailey, TL AU - Church, GM AU - De Moor, B AU - Eskin, E AU - Favorov, AV AU - Frith, MC AU - Fu, Y AU - Kent, WJ AU - Makeev, VJ AU - Mironov, AA AU - Noble, WS AU - Pavesi, G AU - Pesole, G AU - Regnier, M AU - Simonis, N AU - Sinha, S AU - Thijs, G AU - van Helden, J AU - Vandenbogaert, M AU - Weng, Z AU - Workman, C AU - Ye, C AU - Zhu, Z PY - 2005/// ER -

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