New methods for splice site recognition

Sören Sonnenburg, Gunnar Rätsch, Arun Jagota, Klaus Muller

Research output: Chapter in Book/Report/Conference proceedingConference contribution

29 Citations (Scopus)

Abstract

Splice sites are locations in DNA which separate protein-coding regions (exons) from noncoding regions (introns). Accurate splice site detectors thus form important components of computational gene finders. We pose splice site recognition as a classification problem with the classifier learnt from a labeled data set consisting of only local information around the potential splice site. Note that finding the correct position of splice sites without using global information is a rather hard task. We analyze the genomes of the nematode Caenorhabditis elegans and of humans using specially designed support vector kernels. One of the kernels is adapted from our previous work on detecting translation initiation sites in vertebrates and another uses an extension to the well-known Fisher-kernel. We find excellent performance on both data sets.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
PublisherSpringer Verlag
Pages329-336
Number of pages8
Volume2415 LNCS
ISBN (Print)9783540440741
Publication statusPublished - 2002 Jan 1
Externally publishedYes
Event2002 International Conference on Artificial Neural Networks, ICANN 2002 - Madrid, Spain
Duration: 2002 Aug 282002 Aug 30

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume2415 LNCS
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other2002 International Conference on Artificial Neural Networks, ICANN 2002
CountrySpain
CityMadrid
Period02/8/2802/8/30

Fingerprint

Genes
kernel
DNA
Classifiers
Support Vector
Detectors
Proteins
Classification Problems
Genome
Coding
Classifier
Detector
Gene
Protein
Human

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Sonnenburg, S., Rätsch, G., Jagota, A., & Muller, K. (2002). New methods for splice site recognition. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 2415 LNCS, pp. 329-336). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2415 LNCS). Springer Verlag.

New methods for splice site recognition. / Sonnenburg, Sören; Rätsch, Gunnar; Jagota, Arun; Muller, Klaus.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 2415 LNCS Springer Verlag, 2002. p. 329-336 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2415 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Sonnenburg, S, Rätsch, G, Jagota, A & Muller, K 2002, New methods for splice site recognition. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 2415 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2415 LNCS, Springer Verlag, pp. 329-336, 2002 International Conference on Artificial Neural Networks, ICANN 2002, Madrid, Spain, 02/8/28.
Sonnenburg S, Rätsch G, Jagota A, Muller K. New methods for splice site recognition. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 2415 LNCS. Springer Verlag. 2002. p. 329-336. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
Sonnenburg, Sören ; Rätsch, Gunnar ; Jagota, Arun ; Muller, Klaus. / New methods for splice site recognition. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 2415 LNCS Springer Verlag, 2002. pp. 329-336 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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