Title

Fast splice site detection using information content and feature reduction

Document Type

Article

Publication details

Baten, AKMA, Halgamuge, SK & Chang, BCH 2008, 'Fast splice site detection using information content and feature reduction ', BMC Bioinformatics, vol. 9, supp. 12, art. S8.

Published version available from:

http://dx.doi.org/10.1186/1471-2105-9-S12-S8

Peer Reviewed

Peer-Reviewed

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

Additional information

BMC BioinformaticsVolume 9 Supplement 12 Seventh International Conference on Bioinformatics (InCoB2008)

Proceedings Asia Pacific Bioinformatics Network (APBioNet) Seventh International Conference on Bioinformatics (InCoB2008)

Taipei, Taiwan 20-23 October 2008

Edited by Shoba Ranganathan, Wen-Lian Hsu, Ueng-Cheng Yang and Tin Wee Tan