HOVERGEN: Homologous Vertebrate Genes database
duret at evoserv.univ-lyon1.fr
Wed Feb 2 09:54:10 EST 1994
homologous Vertebrate Genes Data Base
Release 4 (22 decembre 1993)
HOVERGEN is a database of homologous vertebrate genes. HOVERGEN allows to easily select sets of homologous genes among a given set of vertebrate species.
HOVERGEN corresponds to the nuclear vertebrate sequences subset of GenBank, with some data corrected, clarified, or completed, notably to address the problem of redundancy. Coding sequences have been classified in gene families. Protein multiple alignments and phylogenetic trees have been calculated for each family.
Sequences and related information have been structured in an ACNUC database. A program named "query" allows to make complex selections in the ACNUC database according to any information clearly declared (keywords, bibliography, taxonomy, etc.). Selection criteria can be combined with boolean operators.
A graphical interface has been developed to visualize and edit trees. Genes are displayed in color, according to their taxonomy. Users have directly access to all information attached to sequences (either from GenBank or specific of HOVERGEN), or 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: phylogenetic trees of gene families, taxonomy, GenBank information and protein multiple alignments.
HOVERGEN is particularly useful for:
- comparative sequence analysis
- molecular evolution studies
More generaly, HOVERGEN gives an overall view of what is known about a particular gene family.
HOVERGEN data and softwares are freely available through anonymous ftp at biom3.univ-lyon1.fr or 220.127.116.11
in the directory /pub/hovergen
Softwares are provided with on-line help. Present version runs on Sun workstations using SunOS or Solaris.
A color screen is recommended.
HOVERGEN is updated at each new GenBank release (every two months). HOVERGEN release 4 (from GenBank 80, December 15 1993) requires 400 Mo of hard disk. A demonstration version of only 4 Mo is also available on our ftp server.
Laboratoire de Biometrie, Genetique et Biologie des Populations
URA CNRS 243 Universite Claude Bernard - Lyon I
43, Bd du 11 Novembre 1918 F-69622 Villeurbanne cedex
Tel: +33 18.104.22.168
E-mail: duret at biomserv.univ-lyon1.fr
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