Databases and Systems

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are computed for all families that have been modified or newly created. The rate of
growth of the database (total amount of sequences) is exponential-like, with a
doubling time of less than two years, but the number of gene families evolves rather
linearly with time (Figure 3).
Figure 3: Evolution of the size of the HOVERGEN database
Database query software
Sequence retrieval
Sequences and annotations are managed using the ACNUC system [22]. This system
is associated with a graphical retrieval software QUERY_WIN, that allows the user
to build complex queries using multiple criteria [23]. Notably, thanks to the
information that we include in HOVERGEN, it is possible to quickly select all
homologous sequences available in a given set of species.
Graphical interface for multiple alignments and phylogenetic trees
We have developed a graphical interface that allows one to simultaneously handle all
the data available in HOVERGEN to analyze homology relationships: phylogenetic
trees, multiple alignments, taxonomic information and sequence annotations (Figure
4). The core of the interface is a phylogenetic tree viewer. Genes are colored
according to the species from which they have been sequenced. The color that are
affected to each taxa are either automatically set for different taxonomic level, or can
be manually chosen by the user. When the user clicks on a gene in the tree, the
sequence definition is displayed in another window. If there are several redundant
sequences for that gene, all definitions are shown. Then, by clicking on a definition