Databases of homologous gene families for comparative genomics.
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/.
Penel
Simon
S
Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Claude Bernard - Lyon 1, 43 bd, du 11 Novembre 1918, 69622 Villeurbanne Cedex, France. penel@biomserv.univ-lyon1.fr
Arigon
Anne-Muriel
AM
Dufayard
Jean-François
JF
Sertier
Anne-Sophie
AS
Daubin
Vincent
V
Duret
Laurent
L
Gouy
Manolo
M
Perrière
Guy
G
D000465:Algorithms; D016000:Cluster Analysis; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D020407:Internet; D010802:Phylogeny; D016415:Sequence Alignment; D012984:Software