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Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach

Firoz Anwar1, Syed Murtuza Baker1*, Taskeed Jabid1, Md Mehedi Hasan2, Mohammad Shoyaib3, Haseena Khan4 and Ray Walshe5*

Author Affiliations

1 Department of Computer Science and Engineering, East West University, Bangladesh

2 Department of Genetic Engineering and Biotechnology, University of Dhaka, Bangladesh

3 Institute of Information Technology, University of Dhaka, Bangladesh

4 Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh

5 Biocomputation Research Group, Dublin City University, Ireland

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BMC Bioinformatics 2008, 9:414  doi:10.1186/1471-2105-9-414

Published: 4 October 2008



Eukaryotic promoter prediction using computational analysis techniques is one of the most difficult jobs in computational genomics that is essential for constructing and understanding genetic regulatory networks. The increased availability of sequence data for various eukaryotic organisms in recent years has necessitated for better tools and techniques for the prediction and analysis of promoters in eukaryotic sequences. Many promoter prediction methods and tools have been developed to date but they have yet to provide acceptable predictive performance. One obvious criteria to improve on current methods is to devise a better system for selecting appropriate features of promoters that distinguish them from non-promoters. Secondly improved performance can be achieved by enhancing the predictive ability of the machine learning algorithms used.


In this paper, a novel approach is presented in which 128 4-mer motifs in conjunction with a non-linear machine-learning algorithm utilising a Support Vector Machine (SVM) are used to distinguish between promoter and non-promoter DNA sequences. By applying this approach to plant, Drosophila, human, mouse and rat sequences, the classification model has showed 7-fold cross-validation percentage accuracies of 83.81%, 94.82%, 91.25%, 90.77% and 82.35% respectively. The high sensitivity and specificity value of 0.86 and 0.90 for plant; 0.96 and 0.92 for Drosophila; 0.88 and 0.92 for human; 0.78 and 0.84 for mouse and 0.82 and 0.80 for rat demonstrate that this technique is less prone to false positive results and exhibits better performance than many other tools. Moreover, this model successfully identifies location of promoter using TATA weight matrix.


The high sensitivity and specificity indicate that 4-mer frequencies in conjunction with supervised machine-learning methods can be beneficial in the identification of RNA pol II promoters comparative to other methods. This approach can be extended to identify promoters in sequences for other eukaryotic genomes.