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Briefings in Functional Genomics and Proteomics Advance Access originally published online on February 20, 2006
Briefings in Functional Genomics and Proteomics 2006 5(1):46-51; doi:10.1093/bfgp/ell011
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© Oxford University Press, 2006, All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

Special Issues Papers

Computational methods for alternative splicing prediction

Paola Bonizzoni, Raffaella Rizzi and Graziano Pesole

Corresponding author. Graziano Pesole, Dipartimento di Biochimica e Biologia Molecolare, Universita di Bari, Via Orabona 4, 70126 Bari, Italy. Tel: +39 080 5929663; Fax: +39 080 5929690. E-mail: graziano.pesole{at}biologia.uniba.it

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


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