Homologous Vertebrate Genes Database

HOVERGEN release 48

Updated on 24 May 2007
Release informations: Protein Nucleotide

Query Hovergen

You can query Hovergen using WWW-Query, Quick Search or CrossTaxa.

Alternatively you can use the following links:
Search by Keyword Protein sequences Nucleotide sequences
Search by Sequence Protein sequences Nucleotide sequences

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.

Content

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 here.

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.

WWW access

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.

Server mirroring

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 procedure.

The whole database is available from our FTP server at URL: 

ftp://pbil.univ-lyon1.fr/pub/hovergen_new/
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 license agreement (See or send an Email to license@isb-sib.ch).

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 interface.

If you use HOVERGEN in a published work, please cite the following reference:

Duret, L., Mouchiroud, D. and Gouy, M. (1994) HOVERGEN, a database of homologous vertebrate genes. Nucleic Acids Res. 22, 2360-2365.

Acknowledgements

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