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This article is part of the supplement: Proceedings of the Fifth Annual MCBIOS Conference. Systems Biology: Bridging the Omics

Open Access Proceedings

Hybrid MM/SVM structural sensors for stochastic sequential data

Brian Roux1 and Stephen Winters-Hilt12*

Author Affiliations

1 Department of Computer Science, University of New Orleans, LA, 70148, USA

2 Research Institute for Children, Children's Hospital, New Orleans, LA, 70148, USA

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BMC Bioinformatics 2008, 9(Suppl 9):S12  doi:10.1186/1471-2105-9-S9-S12

Published: 12 August 2008

Abstract

In this paper we present preliminary results stemming from a novel application of Markov Models and Support Vector Machines to splice site classification of Intron-Exon and Exon-Intron (5' and 3') splice sites. We present the use of Markov based statistical methods, in a log likelihood discriminator framework, to create a non-summed, fixed-length, feature vector for SVM-based classification. We also explore the use of Shannon-entropy based analysis for automated identification of minimal-size models (where smaller models have known information loss according to the specified Shannon entropy representation). We evaluate a variety of kernels and kernel parameters in the classification effort. We present results of the algorithms for splice-site datasets consisting of sequences from a variety of species for comparison.