Homologous Vertebrate Genes Database
HOVERGEN release 48 Updated on 24 May 2007
You can query Hovergen using
Quick Search or
Alternatively you can use the following links:
HOVERGEN is a database of homologous vertebrate genes, structured under
ACNUC sequence database management system.
It allows one to select sets of homologous genes among vertebrate species,
and to visualize multiple alignments and phylogenetic trees. Thus HOVERGEN
is particularly useful for comparative sequence analysis, phylogeny and
molecular evolution studies. More generaly, HOVERGEN gives an overall view
of what is known about a peculiar gene family.
A "cleaned" version of HOVERGEN is as well available at this page
The new version of HOVERGEN
Since April 2002, (release 42) HOVERGEN is build on a new basis.
There are two main differences between the new and the previous version.
First, the new version of HOVERGEN is now build in the same way as HOBACGEN (for more details, click
here, or see the paper on HOBACGEN by Perrière et al. Genome Res 2000 10:379-85).
Secondly, we developped a new graphical interface (named FamFetch). This interface is written
in JAVA and should work on any computer (Mac, PC, UNIX, etc.), and does not require to have the whole database installed locally.
The database itself contains all vertebrate protein sequences from the UniProt Knowledgebase (Swiss-Prot and TrEMBL),
with with some data corrected, clarified or completed (notably to address the problem of redundancy and
orthology/paralogy)and with some annotation modifications.
It contains also all the corresponding nucleotide sequences in EMBL.
Homologous proteins are classified into families and multiple alignments and phylogenetic trees
are computed for each family.
Sequences and related information have been structured in an ACNUC database.
The description on how the database is built is available
Alignmentsfor families containing 2 to 500 sequences have been calculated with MUSCLE .
Phylogenetic trees for families containing 3 to 500 sequences have been calculated with PHYML V3.0
Graphical User Interface
HOVERGEN interface is based on a client/server architecture. To access
the database you only need to install the FamFetch
application on your computer. This program, written in Java, integrates a GUI that allows
users to easily access and visualize:
In FamFetch phylogenetic trees, genes are colored according to the species from which they come. The user can modify the color table according to the taxa (any taxonomic level) he is interested in. This color table is saved in a file of preferences (named .famfetch in UNIX (UNIX, Linux, Mac OS X), FamFetch.Prefs in MaOS 9 (or earlier), FamFetch.ini in Windows systems). The color table that is installed by default with FamFetch is dedicated to prokaryotes (for the HOBACGEN database). You can replace this preference file by the one we have prepared for vertebrates, that is available here.
- The list of the families available in the database.
- The sequence (protein or nucleotide) of the genes
defining these families.
- The alignments built with these families.
- The phylogenetic trees computed with these alignments.
It is also possible to query the database on this server through the
WWW-Query system. Note that
HOVERGEN is splitted into two databases on this server: HOVERGEN
contains the protein sequences from the UniProt Knowledgebase (Swiss-Prot and TrEMBL) HOVERGENDNA
contains the nucleotide sequences from EMBL.
You don't need to install the server itself to have HOVERGEN running on your
computer as the client is enough for that purpose. On the other hand
you may want to set-up your own server in a way to speed up your
database access and to propose that service to potential users in your
geographic area. To install an HOVERGEN server, you need first to
register. Starting from the
registering page results, you will have access to the server installation
The whole database is available from our FTP server at URL:
Note that it is much more efficient to use a dedicated FTP client to download the
database rather than an Internet Web browser.
Important note: the SWISS-PROT entries such as those found in HOVERGEN are
copyrighted. They are produced through a collaboration between the Swiss Institute
of Bioinformatics and the European Bioinformatics Institute. There are no restrictions
on its use by non-profit institutions as long as its content is in no way modified.
Usage by and for commercial entities requires a
(See or send an Email to firstname.lastname@example.org).
Contact and reference
If you encounter some problems when installing or using HOVERGEN, please
contact Laurent Duret.
Also we welcome any comments or suggestions on the database and/or its
If you use HOVERGEN in a published work, please cite the following
Duret, L., Mouchiroud, D. and Gouy, M. (1994) HOVERGEN, a database of homologous vertebrate
genes. Nucleic Acids Res. 22, 2360-2365.
If you have problems or comments...
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