Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
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 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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Heber, S.
Right arrow Articles by Pevzner, P. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Heber, S.
Right arrow Articles by Pevzner, P. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 18 no. 90001 2002
Pages S181-S188
© 2002 Oxford University Press

Splicing graphs and EST assembly problem

Steffen Heber , Max Alekseyev , Sing-Hoi Sze , Haixu Tang and Pavel A. Pevzner

Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, 92093-0114, USA

Received on January 24, 2002 ; revised on April 1, 2002 ; accepted on April 1, 2002

Motivation: The traditional approach to annotate alternative splicing is to investigate every splicing variant of the gene in a case-by-case fashion. This approach, while useful, has some serious shortcomings. Recent studies indicate that alternative splicing is more frequent than previously thought and some genes may produce tens of thousands of different transcripts. A list of alternatively spliced variants for such genes would be difficult to build and hard to analyse. Moreover, such a list does not show the relationships between different transcripts and does not show the overall structure of all transcripts. A better approach would be to represent all splicing variants for a given gene in a way that captures the relationships between different splicing variants.

Results: We introduce the notion of the splicing graph that is a natural and convenient representation of all splicing variants. The key difference with the existing approaches is that we abandon the linear (sequence) representation of each transcript and replace it with a graph representation where each transcript corresponds to a path in the graph. We further design an algorithm to assemble EST reads into the splicing graph rather than assembling them into each splicing variant in a case-by-case fashion.

Availability: http://www-cse.ucsd.edu/groups/bioinformatics/software.html

Contact: sheber{at}ucsd.edu

Keywords: EST assembly; splicing graph; alternative splicing


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
 BioinformaticsHome page
E. D. Harrington and P. Bork
Sircah: a tool for the detection and visualization of alternative transcripts
Bioinformatics, September 1, 2008; 24(17): 1959 - 1960.
[Abstract] [Full Text] [PDF]

Home page
 Biol. Bull.Home page
R. M. Freeman JR., M. Wu, M-M. Cordonnier-Pratt, L. H. Pratt, C. E. Gruber, M. Smith, E. S. Lander, N. Stange-Thomann, C. J. Lowe, J. Gerhart, et al.
cDNA Sequences for Transcription Factors and Signaling Proteins of the Hemichordate Saccoglossus kowalevskii: Efficacy of the Expressed Sequence Tag (EST) Approach for Evolutionary and Developmental Studies of a New Organism
Biol. Bull., June 1, 2008; 214(3): 284 - 302.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. B. Gerstein, C. Bruce, J. S. Rozowsky, D. Zheng, J. Du, J. O. Korbel, O. Emanuelsson, Z. D. Zhang, S. Weissman, and M. Snyder
What is a gene, post-ENCODE? History and updated definition
Genome Res., June 1, 2007; 17(6): 669 - 681.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
S. Tanner, Z. Shen, J. Ng, L. Florea, R. Guigo, S. P. Briggs, and V. Bafna
Improving gene annotation using peptide mass spectrometry
Genome Res., February 1, 2007; 17(2): 231 - 239.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Bollina, B. T. K. Lee, T. W. Tan, and S. Ranganathan
ASGS: an alternative splicing graph web service.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W444 - W447.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Xing, T. Yu, Y. N. Wu, M. Roy, J. Kim, and C. Lee
An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs
Nucleic Acids Res., June 6, 2006; 34(10): 3150 - 3160.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
P. Bonizzoni, R. Rizzi, and G. Pesole
Computational methods for alternative splicing prediction
Brief Funct Genomic Proteomic, March 1, 2006; 5(1): 46 - 51.



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.