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Nucleic Acids Research Advance Access published online on April 8, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn153
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Exalign: a new method for comparative analysis of exon–intron gene structures

Giulio Pavesi1, Federico Zambelli1, Corrado Caggese2 and Graziano Pesole3,4,*

1Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan, Milan, 2Dipartimento di Genetica e Microbiologia, University of Bari, Bari, 3Dipartimento di Biochimica e Biologia Molecolare "E. Quagliariello", University of Bari, Bari and 4Istituto Tecnologie Biomediche – Consiglio Nazionale delle Ricerche, Bari, Italy

*To whom correspondence should be addressed. Tel: +39 80 5443588; Fax: +39 80 5443317; Email: graziano.pesole{at}biologia.uniba.it

Received January 7, 2008. Revised March 16, 2008. Accepted March 19, 2008.

The evolution of genes is usually studied and reconstructed at the sequence level, that is, by comparing and aligning their genomic, transcript or protein sequences. However, including the exon–intron structure of genes in the analysis can provide further and useful information, for example to draw reliable phylogenetic relationships left unsolved by traditional sequence-based evolutionary studies, or to shed further light on patterns of intron gain and loss. In spite of this, no tool especially devised for this task is currently available. In this work we present Exalign, an algorithm designed to retrieve, compare and search for the exon-intron structure of existing gene annotations, that has been implemented in a software tool freely accessible through a web interface as well as available for download. We present different applications of our method, from the reconstruction of the evolutionary history of homologous gene families to the detection of as of today unknown cases of intron loss in human and rodents, and, remarkably, two never reported intron gain events in human and mouse. The web interface for accessing Exalign is available at http://www.pesolelab.it/exalign/ or http://www.beacon.unimi.it/exalign/

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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