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Nucleic Acids Research 2004 32(13):3977-3983; doi:10.1093/nar/gkh731
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Published online 3 August 2004

Nucleic Acids Research, Vol. 32 No. 13 © Oxford University Press 2004; all rights reserved

The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome

Jeremy Leipzig, Pavel Pevzner1 and Steffen Heber*

Department of Computer Science, College of Engineering, North Carolina State University, Raleigh, NC 27695-7566, USA and 1 Department of Computer Science & Engineering, APM 4802, University of California, San Diego, La Jolla, CA 92093-0114, USA

* To whom correspondence should be addressed. Tel: +1 919 513 2726; Fax: +1 919 513 7315; Email: sheber{at}ncsu.edu

Received January 5, 2004; Revised March 14, 2004; Accepted July 12, 2004

Alternative splicing essentially increases the diversity of the transcriptome and has important implications for physiology, development and the genesis of diseases. Conventionally, alternative splicing is investigated in a case-by-case fashion, but this becomes cumbersome and error prone if genes show a huge abundance of different splice variants. We use a different approach and integrate all transcripts derived from a gene into a single splicing graph. Each transcript corresponds to a path in the graph, and alternative splicing is displayed by bifurcations. This representation preserves the relationships between different splicing variants and allows us to investigate systematically all possible putative transcripts. We built a database of splicing graphs for human genes, using transcript information from various major sources (Ensembl, RefSeq, STACK, TIGR and UniGene). A Web interface allows users to display the splicing graphs, to interactively assemble transcripts and to access their sequences as well as neighboring genomic regions. We also provide for each gene an exhaustive pre-computed catalog of putative transcripts—in total more than 1.2 million sequences. We found that ~65% of the investigated genes show evidence for alternative splicing, and in 5% of the cases, a single gene might produce over 100 transcripts.


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