Introduction

Identification of DNA-binding proteins is essential in studying cellular activities as the DNA-binding proteins play a pivotal role in gene regulation. In this study, we propose newDNA-Prot, a DNA-binding protein predictor that employs support vector machine classifier and a comprehensive feature representation. The sequence representation are categorized into 6 groups: primary sequence based, evolutionary profile based, predicted secondary structure based, predicted relative solvent accessibility based, physicochemical property based and biological function based features. The mRMR, wrapper and two-stage feature selection methods are employed for removing irrelevant features and reducing redundant features. Experiments demonstrate that the two-stage method performs better than the mRMR and wrapper methods. We also perform a statistical analysis on the selected features and results show that more than 95% of the selected features are statistically significant and they cover all 6 feature groups. The newDNA-Prot method is compared with several state of the art algorithms, including iDNA-Prot, DNAbinder and DNA-Prot. The results demonstrate that newDNA-Prot method outperforms the iDNA-Prot, DNAbinder and DNA-Prot methods. More specific, newDNA-Prot improves the runner-up method, DNA-Prot for around 10% on several evaluation measures. The proposed newDNA-Prot method is available at http://sourceforge.net/projects/newdnaprot/

Publications

  1. newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation.
    Cite this
    Zhang Y, Xu J, Zheng W, Zhang C, Qiu X, Chen K, Ruan J, 2014-10-01 - Computational biology and chemistry

Credits

  1. Yanping Zhang
    Developer

    Department of Mathematics, School of Science

  2. Jun Xu
    Developer

    College of Mathematical Sciences and LPMC, Nankai University

  3. Wei Zheng
    Developer

    College of Mathematical Sciences and LPMC, Nankai University

  4. Chen Zhang
    Developer

    College of Mathematical Sciences and LPMC, Nankai University

  5. Xingye Qiu
    Developer

    College of Mathematical Sciences and LPMC, Nankai University

  6. Ke Chen
    Developer

    School of Computer Science and Software Engineering, Tianjin Polytechnic University

  7. Jishou Ruan
    Investigator

    College of Mathematical Sciences and LPMC, Nankai University

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Summary
AccessionBT005382
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByJishou Ruan