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This article is part of the supplement: Seventh International Conference on Bioinformatics (InCoB2008)

Open Access Research

Fast splice site detection using information content and feature reduction

AKMA Baten1*, SK Halgamuge1 and BCH Chang2

Author Affiliations

1 Biomechanical Engineering Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Victoria 3010, Australia

2 Institute of Plant and Microbial Biology, Academia Sinica, Taiwan

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BMC Bioinformatics 2008, 9(Suppl 12):S8  doi:10.1186/1471-2105-9-S12-S8

Published: 12 December 2008

Abstract

Background

Accurate identification of splice sites in DNA sequences plays a key role in the prediction of gene structure in eukaryotes. Already many computational methods have been proposed for the detection of splice sites and some of them showed high prediction accuracy. However, most of these methods are limited in terms of their long computation time when applied to whole genome sequence data.

Results

In this paper we propose a hybrid algorithm which combines several effective and informative input features with the state of the art support vector machine (SVM). To obtain the input features we employ information content method based on Shannon's information theory, Shapiro's score scheme, and Markovian probabilities. We also use a feature elimination scheme to reduce the less informative features from the input data.

Conclusion

In this study we propose a new feature based splice site detection method that shows improved acceptor and donor splice site detection in DNA sequences when the performance is compared with various state of the art and well known methods.