HOVERGEN: homologous vertebrate genes db - new release
duret at evol10.univ-lyon1.fr
Mon Feb 28 10:45:41 EST 1994
//////////////////////////// New Release //////////////////////////////////
homologous Vertebrate Genes Data Base
Release 5 (28 February 1994)
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 5
(from GenBank 81, February 15 1994) 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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