Abstract
BackgroundComparative 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.MethodsWe 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.ResultsThree 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 .
Highlights
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 and phylogenetics
For HOMOLENS, nucleotide annotated sequences come from Ensembl and protein sequences are generated from the corresponding Coding DNA Sequences (CDS) described in Ensembl annotations
Tree reconciliation The main originality of our system is the possibility to make queries using tree patterns, as this allows users to search for orthologs and for Horizontal Gene Transfers (HGTs), gene duplications or any phylogenetic profile of interest
Summary
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. HOVERGEN, a database devoted to homologous gene families in vertebrates [1,2] has been first released in 1994. HOGENOM contains homologous gene families from all available complete genomes from bacteria, archaea and unicellular eukaryotes, plus some representative plants and animals. HOMOLENS contains gene families from complete animal genomes found in Ensembl [13]. After family assembly, protein sequences are aligned and the alignments produced are used to build phylogenetic trees. Those two steps are realized through an automated procedure
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