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  Accurate Splice site Prediction Using Support Vector Machines

Sonnenburg, S., Schweikert, G., Philips, P., Behr, J., & Rätsch, G. (2007). Accurate Splice site Prediction Using Support Vector Machines. BMC Bioinformatics, 8(Supplement 10), 1-16.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0013-CAE1-8 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-B9B1-4
Genre: Conference Paper

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 Creators:
Sonnenburg, S, Author              
Schweikert, G1, 2, 3, Author              
Philips , P3, Author
Behr, J3, Author
Rätsch, G3, Author              
Affiliations:
1Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497794              
2Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497795              
3Friedrich Miescher Laboratory, Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, DE, ou_2575692              

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 Abstract: Background: For splice site recognition, one has to solve two classification problems: discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems typically rely on Markov Chains to solve these tasks. Results: In this work we consider Support Vector Machines for splice site recognition. We employ the so-called weighted degree kernel which turns out well suited for this task, as we will illustrate in several experiments where we compare its prediction accuracy with that of recently proposed systems. We apply our method to the genome-wide recognition of splice sites in Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Danio rerio, and Homo sapiens. Our performance estimates indicate that splice sites can be recognized very accurately in these genomes and that our method outperforms many other methods including Markov Chains, GeneSplicer and SpliceMachine. We provide genome-wide predictions of splice sites and a stand-alone prediction tool ready to be used for incorporation in a gene finder. Availability: Data, splits, additional information on the model selection, the whole genome predictions, as well as the stand-alone prediction tool are available for download at http:// www.fml.mpg.de/raetsch/projects/splice.

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 Dates: 2007-12
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1186/1471-2105-8-S10-S7
BibTex Citekey: 4809
 Degree: -

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Title: NIPS 2006 Workshop on New Problems and Methods in Computational Biology
Place of Event: Whistler, Canada
Start-/End Date: 2006-12-08

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Title: BMC Bioinformatics
Source Genre: Journal
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Publ. Info: BioMed Central
Pages: - Volume / Issue: 8 (Supplement 10) Sequence Number: - Start / End Page: 1 - 16 Identifier: ISSN: 1471-2105
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905000