Splicing graph is an efficient way of representing gene structure and alternative splicing information. It treats the gene structure as a partial order graph (directed acylic graph), in which the exons are represented as nodes and introns are represented as edges. Splicing graph has been useful in EST assembly, especially in dealing with alternative splicing. Please check out the following papers if you are interested:
Splicing graphs and EST assembly problem Heber S et.al., Bioinformatics, 2002
Generating consensus sequences from partial order multiple sequence alignment graphs Lee C, Bioinformatics, 2003
I had spent some time in the past to use splicing graphs to construct multiple isoforms for alternatively spliced genes using EST data. Here is the paper.
Posted by yxing at March 25, 2005 10:38 AM