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Briefings in Functional Genomics and Proteomics Advance Access published online on February 20, 2006
Briefings in Functional Genomics and Proteomics, doi:10.1093/bfgp/ell011
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© The Author 2006. Published by Oxford University Press. All rights reserved. For permissions please email: journals.permissions@oxfordjournals.org

Paper

Joining high-throughput technology with in silico modelling advances genome-wide screening towards targeted discovery

Paola Bonizzoni, Raffaella Rizzi, and Graziano Pesole *

* To whom correspondence should be addressed.
Graziano Pesole, E-mail: graziano.pesole{at}biologia.uniba.it


  Abstract

The fact that a large majority of mammalian genes are subject to alternative splicing indicates that this phenomenon represents a major mechanism for increasing proteome complexity.

Here, we provide an overview of current methods for the computational prediction of alternative splicing based on the alignment of genome and transcript sequences. Specific features and limitations of different approaches and software are discussed, particularly those affecting prediction accuracy and assembly of alternative transcripts.

Keywords: alternative splicing; gene regulation; algorithm; software; comparative genomics.

Paola Bonizzoni is an Associate Professor of Computer Science at the University of Milano-Bicocca in Milan. Her research interests are mainly in the area of Theoretical Computer Science, and include computational complexity, models in biomolecular computation and combinatorial algorithms in Computational Biology.

Raffaella Rizzi has currently a postdoc position in Computer Science at the University of Milan-Bicocca. Her research interests include computational models in molecular biology, gene expression and DNA microarrays.

Graziano Pesole is a Full Professor of Molecular Biology at the University of Bari, leading a research group in Bioinformatics and Comparative Genomics. His research interests include bioinformatics tools for genome annotation and molecular evolution.


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