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This article is part of the supplement: European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration. Leading applications and technologies in bioinformatics

Open Access Proceedings

Databases of homologous gene families for comparative genomics

Simon Penel1, Anne-Muriel Arigon2, Jean-François Dufayard2, Anne-Sophie Sertier1, Vincent Daubin1, Laurent Duret1, Manolo Gouy1 and Guy Perrière1*

Author Affiliations

1 Laboratoire de Biométrie et Biologie Évolutive, CNRS, Université Claude Bernard – Lyon 1, 43 bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France

2 Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, 161 rue Ada, 34392 Montpellier, France

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BMC Bioinformatics 2009, 10(Suppl 6):S3  doi:10.1186/1471-2105-10-S6-S3

Published: 16 June 2009

Abstract

Background

Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary processes at the molecular level (speciation, single gene or whole genome duplications, etc.) and phylogenetics. In that context, databases providing users high quality homologous families and sequence alignments as well as phylogenetic trees based on state of the art algorithms are becoming indispensable.

Methods

We developed an automated procedure allowing massive all-against-all similarity searches, gene clustering, multiple alignments computation, and phylogenetic trees construction and reconciliation. The application of this procedure to a very large set of sequences is possible through parallel computing on a large computer cluster.

Results

Three databases were developed using this procedure: HOVERGEN, HOGENOM and HOMOLENS. These databases share the same architecture but differ in their content. HOVERGEN contains sequences from vertebrates, HOGENOM is mainly devoted to completely sequenced microbial organisms, and HOMOLENS is devoted to metazoan genomes from Ensembl. Access to the databases is provided through Web query forms, a general retrieval system and a client-server graphical interface. The later can be used to perform tree-pattern based searches allowing, among other uses, to retrieve sets of orthologous genes. The three databases, as well as the software required to build and query them, can be used or downloaded from the PBIL (Pôle Bioinformatique Lyonnais) site at http://pbil.univ-lyon1.fr/ webcite.