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Nucleic Acids Research Advance Access published online on May 29, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp449
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors

Wen-Yi Chu1, Yu-Feng Huang1, Chun-Chin Huang2, Yi-Sheng Cheng3, Chien-Kang Huang2,* and Yen-Jen Oyang1,4,5,*

1Department of Computer Science and Information Engineering, 2Department of Engineering Science and Ocean Engineering, 3Department of Life Science, 4Graduate Institute of Biomedical Electronics and Bioinformatics, and 5Center for Systems Biology and Bioinformatics, National Taiwan University, Taipei, Taiwan, ROC

*To whom correspondence should be addressed. Tel: +886 2 3366 5736; Fax: +886 2 2392 9885; Email: ckhuang{at}ntu.edu.tw Correspondence may also be addressed to Dr Yen-Jen Oyang. Tel: +886 2 3366 4888; Email: yjoyang{at}csie.ntu.edu.tw

Received March 4, 2009. Revised May 11, 2009. Accepted May 12, 2009.

This article presents the design of a sequence-based predictor named ProteDNA for identifying the sequence-specific binding residues in a transcription factor (TF). Concerning protein–DNA interactions, there are two types of binding mechanisms involved, namely sequence-specific binding and nonspecific binding. Sequence-specific bindings occur between protein sidechains and nucleotide bases and correspond to sequence-specific recognition of genes. Therefore, sequence-specific bindings are essential for correct gene regulation. In this respect, ProteDNA is distinctive since it has been designed to identify sequence-specific binding residues. In order to accommodate users with different application needs, ProteDNA has been designed to operate under two modes, namely, the high-precision mode and the balanced mode. According to the experiments reported in this article, under the high-precision mode, ProteDNA has been able to deliver precision of 82.3%, specificity of 99.3%, sensitivity of 49.8% and accuracy of 96.5%. Meanwhile, under the balanced mode, ProteDNA has been able to deliver precision of 60.8%, specificity of 97.6%, sensitivity of 60.7% and accuracy of 95.4%. ProteDNA is available at the following websites:

http://protedna.csbb.ntu.edu.tw/

http://protedna.csie.ntu.edu.tw/

http://bio222.esoe.ntu.edu.tw/ProteDNA/.


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