Skip Navigation


Bioinformatics Advance Access originally published online on November 5, 2004
Bioinformatics 2005 21(7):897-901; doi:10.1093/bioinformatics/bti132
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/7/897    most recent
bti132v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (32)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Dror, G.
Right arrow Articles by Shamir, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Dror, G.
Right arrow Articles by Shamir, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Accurate identification of alternatively spliced exons using support vector machine

Gideon Dror 1,*, Rotem Sorek 2,3 and Ron Shamir 4

1The Academic College of Tel-Aviv-Yaffo Tel Aviv 4044, Israel
2Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University Tel Aviv 69978, Israel
3Compugen Tel Aviv 69512, Israel
4School of Computer Science, Tel Aviv University Tel Aviv 69073, Israel

*To whom correspondence should be addressed.

Motivation: Alternative splicing is a major component of the regulatory action on mammalian transcriptomes. It is estimated that over half of all human genes have more than one splice variant. Previous studies have shown that alternatively spliced exons possess several features that distinguish them from constitutively spliced ones. Recently, we have demonstrated that such features can be used to distinguish alternative from constitutive exons. In the current study, we used advanced machine learning methods to generate robust classifier of alternative exons.

Results: We extracted several hundred local sequence features of constitutive as well as alternative exons. Using feature selection methods we find seven attributes that are dominant for the task of classification. Several less informative features help to slightly increase the performance of the classifier. The classifier achieves a true positive rate of 50% for a false positive rate of 0.5%. This result enables one to reliably identify alternatively spliced exons in exon databases that are believed to be dominated by constitutive exons.

Availability: Upon request from the authors.

Contact: gideon{at}mta.ac.il


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
M. Akerman and Y. Mandel-Gutfreund
Does distance matter? Variations in alternative 3' splicing regulation
Nucleic Acids Res., August 17, 2007; (2007) gkm603v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Nikolajewa, R. Pudimat, M. Hiller, M. Platzer, and R. Backofen
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W688 - W693.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. L. S. Ng and S. K. Mishra
De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
Bioinformatics, June 1, 2007; 23(11): 1321 - 1330.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Xia, J. Bi, and Y. Li
Identification of alternative 5'/3' splice sites based on the mechanism of splice site competition
Nucleic Acids Res., December 4, 2006; 34(21): 6305 - 6313.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Akerman and Y. Mandel-Gutfreund
Alternative splicing regulation at tandem 3' splice sites
Nucleic Acids Res., January 3, 2006; 34(1): 23 - 31.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Hiller, K. Huse, M. Platzer, and R. Backofen
Non-EST based prediction of exon skipping and intron retention events using Pfam information
Nucleic Acids Res., October 4, 2005; 33(17): 5611 - 5621.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. Baek and P. Green
Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing
PNAS, September 6, 2005; 102(36): 12813 - 12818.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.