HOVERGEN - A DATABASE OF HOMOLOGOUS VERTEBRATE GENES

Comparison of homologous genes is a major step for many studies relate d to genome structure, function or evolution. Similarity search progra ms easily find genes homologous to a given sequence. However, only ver y tedious manual procedures allow the retrieval of all sets of homolog ous genes sequenced for a given set of species. Moreover, this search often generates errors due to the complexity of data to be managed sim ultaneously: phylogenetic trees, alignments, taxonomy, sequences and r elated information. HOVERGEN helps to solve these problems by integrat ing all this information. HOVERGEN corresponds to GenBank sequences fr om all vertebrate species, with some data corrected, clarified, or com pleted, notably to address the problem of redundancy. Coding sequences have been classified in gene families. Protein multiple alignments an d phylogenetic trees have been calculated for each family. Sequences a nd related information have been structured in an ACNUC database which permits complex selections. A graphical interface has been developed to visualize and edit trees. Genes are displayed in color, according t o their taxonomy. Users have directly access to all information attach ed to sequences and to multiple alignments simply by clicking on genes . This graphical tool gives thus a rapid and simple access to all data necessary to interpret homology relationships between genes. HOVERGEN allows the user to easily select sets of homologous vertebrate genes, and thus is particularly useful for comparative sequence analysis, or molecular evolution studies.