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2016 | OriginalPaper | Chapter

An Adaptive Weighted Degree Kernel to Predict the Splice Site

Authors : Tianqi Wang, Ke Yan, Yong Xu, Jinxing Liu

Published in: Biometric Recognition

Publisher: Springer International Publishing

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Abstract

The weighted degree kernel is a good means to predict the splice site. Its prediction performance is affected by positions in the DNA sequence of nucleotide bases. Based on this fact, we propose confusing positions in this article. Using the confusing positions and the key positions which we proposed in previous work, we construct a weight array to obtain adaptive weighted degree kernel, a kind of string kernel to predict the splice site. Then to prove the efficient and advance of the method, we use the public available dataset to train support vector machines to compare the performance of the adaptive weighted degree kernel and conventional weighted degree kernel. The results show that the adaptive weighted degree kernel has better performance than the weighted degree kernel.

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next chapter The Prediction of Human Genes in DNA Based on a Generalized Hidden Markov Model
Literature
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Baten, A.K.M.A., Halgamuge, S.K., Chang, B., Wickramarachchi, N.: Biological sequence data preprocessing for classification: a case study in splice site identification. In: Liu, D., Fei, S., Hou, Z., Zhang, H., Sun, C. (eds.) ISNN 2007, Part II. LNCS, vol. 4492, pp. 1221–1230. Springer, Heidelberg (2007)CrossRef
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Sören, S., et al.: Accurate splice site prediction using support vector machines. BMC Bioinform. 8(Suppl. 10), S7 (2007)
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Baten, K.M.A.A., Halgamuge, S.K., Chang, B.C.H.: Fast splice site detection using information content and feature reduction. BMC Bioinform. 9(Suppl. 12), S8 (2008)CrossRef
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Sören, S., Rätsch, G., Rieck, K.: Large scale learning with string kernels. In: Large Scale Kernel Machines, pp. 73–103 (2007)
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Pollastro, P., Rampone, S.: HS3D, a dataset of Homo Sapiens splice regions, and its extraction procedure from a major public database. Int. J. Mod. Phys. C 13(08), 1105–1117 (2002)CrossRef
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Metadata
Title
An Adaptive Weighted Degree Kernel to Predict the Splice Site
Authors
Tianqi Wang
Ke Yan
Yong Xu
Jinxing Liu
Copyright Year
2016
Book
Biometric Recognition

Print ISBN: 978-3-319-46653-8

Electronic ISBN: 978-3-319-46654-5

Copyright Year: 2016

DOI
https://doi.org/10.1007/978-3-319-46654-5_81

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