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Briefings in Bioinformatics Advance Access published online on February 3, 2006
Briefings in Bioinformatics, 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
Received August 3, 2005
Accepted December 6, 2005

Original Article

Bioinformatics of alternative splicing and its regulation

Liliana Florea *

* To whom correspondence should be addressed.
Liliana Florea, E-mail: florea{at}gwu.edu


  Abstract

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.
Liliana Florea is an Assistant Professor of Computer Science at the George Washington University. She develops algorithms and software for aligning cDNA and genomic sequences and for annotating genes and alternative splicing.
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