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Briefings in Bioinformatics Advance Access originally published online on February 3, 2006
Briefings in Bioinformatics 2006 7(1):55-69; doi:10.1093/bib/bbk005
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© The Author 2006. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Bioinformatics of alternative splicing and its regulation

Liliana Florea

Liliana D. Florea, Department of Computer Science, George Washington Univeristy, Academic Center-Rm 714, Washington DC 20052. Tel: (202) 994-1057; Fax (202) 994-4875; florea{at}gwu.edu

The sequencing of the human genome and ensuing wave of data generation have brought new light upon the extent and importance of alternative splicing as an RNA regulatory mechanism. Alternative splicing could potentially explain the complexity of protein repertoire during evolution, and defects in the splicing mechanism are responsible for diseases as complex as cancer. Among the challenges that rise in light of these discoveries are cataloguing splice variation in the human and other eukaryotic genomes, and identifying and characterizing the splicing regulatory elements that control their expression. Bioinformatics efforts tackling these two questions are just at the beginning. This article is a survey of these methods.

Keywords: alternative splicing, gene indices, genome-based clustering, splice graph, splicing enhancers, splicing silencers


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