HOBACGEN: Database system for comparative genomics in bacteria

We present here HOBACGEN, a database system devoted to comparative genomics in bacteria. HOBACGEN contains all available protein genes from bacteria, archaea, and yeast, taken from SWISS-PROT/TrEMBL and classified into famili es. It also includes multiple alignments and phylogenetic trees built from these families. The database is organized under a client/server architectur e with a client written in lava, which may run on any platform. This client integrates a graphical interface allowing users to select families accordi ng to various criteria and notably to select homologs common to a given set of taxa. This interface also allows users to visualize multiple alignments and trees associated to families. In tree displays, protein gene names are colored according to the taxonomy of the corresponding organisms. Users ma y access all information associated to sequences and multiple alignments by clicking on genes. This graphic tool thus gives a rapid and simple access to all data required to interpret homology relationships between genes and distinguish orthologs from paralogs. Instructions for installation of the c lient or the server are available at http://pbil.univ-lyonl.fr/databases/ho bacgen.html.