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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


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