Plant Genome II Conference
Town & Country Conference Center, San Diego, CA, January, 1994.
PG-II: A SOFTWARE TO MANAGE cDNA ARABIDOPSIS SEQUENCES AND RELATED
DATA
A SOFTWARE TO MANAGE cDNA ARABIDOPSIS SEQUENCES AND RELATED
DATA
J.L. Charpenteau(*), M.F. Jourjon(*) and C. Christophe(**)
(*) INRA Station de Biometrie et Intelligence Artificielle BP 27
31326 CASTANET TOLOSAN FRANCE
(**) INRA Direction de l'informatique 147 Rue de l'Universite
75341 PARIS FRANCE
Begun in 1991, the french cDNA Arabidopsis Thaliana
sequencing effort involves nine teams located throughout the
country. This geographical design requires a special effort in
realizing a computer system dedicated to maintain the data files.
The data are concerned with sequences, experimental conditions
and associated features of clone libraries used during the
sequencing effort. Such a computer system is devoted to several
tasks: avoiding useless redundancy in the sequencing by
collecting and comparing sequences; managing the submitted
sequences and more generally the communications with
international databases; making available all the public
data on the Arabidopsis genome through a friendly interface, and
making available software tools for the analysis of sequences and
data (through an interface with GCG for example). This computer
system is running on UNIX SUN workstations in each laboratory.
These workstations are connected to the server in Toulouse
through the academic french network (RENATER 64kb). The
computer system consists of two parts: in Toulouse, an object
oriented database management system collects and updates all the
data from the sequencing effort; In addition, it has to insure
exchanges with the international databases. The inputs and
modifications are realized in each laboratory through an Xwindow
interface. Also, the AATDB software has been modified in order
to make available with the same tool both our data and the public
data. These "modified AATDB" will be updated weekly by the
central database. At the end of 1993, the database contains
about 3000 sequences and related from about 10 clones libraries,
9 teams and 40 scientists. Most of these data are in the EMBL
database.
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