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. Here 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/

Exalign: a new method for comparative analysis of exon–intron gene structures / F. Zambelli, G. Pavesi, G. Pesole. ((Intervento presentato al 10. convegno FISV Annual Congress tenutosi a Riva del Garda (TN) nel 2008.

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

F. Zambelli
Primo
;
G. Pavesi
Secondo
;
G. Pesole
Ultimo
2008

Abstract

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. Here 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/
2008
Settore INF/01 - Informatica
Federazione Italiana Scienze della Vita
http://hdl.handle.net/2434/39380
Exalign: a new method for comparative analysis of exon–intron gene structures / F. Zambelli, G. Pavesi, G. Pesole. ((Intervento presentato al 10. convegno FISV Annual Congress tenutosi a Riva del Garda (TN) nel 2008.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/62805
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