|Paper:||"Splicing graphs and EST assembly problem."|
|Abstract||Splicing graphs and EST assembly problem
Steffen Heber, Max Alekseyev, Sing-Hoi Sze, Haixu Tang and Pavel A.
Department of Computer Science & Engineering, University of California,
San Diego, La Jolla, CA, 92093-0114, USA
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