Arabidopsis genome database now available
Mike Cherry 726-5955
CHERRY at Frodo.MGH.Harvard.EDU
Fri Jul 10 15:14:21 EST 1992
The first release of the Arabidopsis genome database, AAtDB, is now
AAtDB, An Arabidopsis thaliana Data Base, uses the excellent database
software written by Richard Durbin (MCR-LMB, UK) and Jean Thierry-Mieg
(CNRS, France). AAtDB is funded by the U. S. Department of
Agriculture Plant Genome Research Program through the National
Agricultural Library and is maintained by a group at the Massachusetts
General Hospital and Harvard Medical School.
AAtDB is available free of charge via Internet network transfer. A
complete description of the procedure to retrieve the software and
database is included in a separate message.
The ACeDB software allows the user to browse information by simply
pointing and clicking with the workstation mouse. A powerful query
facility is also available. However, our experience is that most users
choose the mouse interface to find the information they are interested in.
Currently AAtDB contains:
- The Hauge/Goodman cosmid/YAC physical map including >14,000
- Genetic markers, both RFLP and classical markers.
- Unified Genetic Map. Including both the Goodman and Meyerowitz
RFLP markers and classical genetic markers.
- Primary F2 mapping database from the Goodman and Meyerowitz RFLP
- Primary two point recombination data from M. Koornneef.
- A strain catalog including all strains and clones available
from the Nottingham Stock Centre and the ABRC at Ohio State
- Bibliographic citations from 1964 to present, currently
numbering over 2,600.
- List of Arabidopsis researchers including mail address, phone
number, FAX number and electronic mail address. Currently
information on over 500 colleagues is included.
- Green Book. The Green Book by Meyerowitz and Pruitt has been
updated and integrated into many parts of the database,
including phenotype and allele descriptions.
- All Arabidopsis DNA sequences from GenBank, currently there are
over 300 sequences.
- BLASTX defined amino acid sequence similarities for all
Arabidopsis sequences against the SwissProt, PIR and GenPept
protein sequence databases.
- REBASE restriction enzyme database maintained by R. Roberts,
- Graphical displays of all Genetic Maps, Physical Maps, and DNA
Sequence features and similarities.
- Scanned images of photographs showing mutant phenotypes.
As much as possible all information is connected to other information in
the database. The database presents the information in separate windows
that allow many parts of the database to be viewed at one time. There
are also many paths to any piece of information, allowing the user to
easily navigate the connections between the various types of
This is just the starting point. Just as the known Arabidopsis genome
information is always being expanded AAtDB is also being extended and
enhanced via periodic updates. There is much more information that we
are working to include in subsequent updates of AAtDB.
The database currently requires a Unix workstation running X-Windows.
Versions of the ACeDB database software are available for Sun
Microsystems SPARCstations, Digital Equipment's DECstation, Silicon
Graphics Iris series and NeXT workstations.
A printed manual "An Introduction to ACeDB: For AAtDB, An Arabidopsis
thaliana database" is available on request from the MGH group. While
this manual is not required to use the database many people have found
it very useful as a beginning tutorial for the ACeDB software.
A Macintosh version of the ACeDB software is under development. We are
currently using an alpha version of the sofware and are very impressed.
A public release version is expected within six months.
An interactive text based version of AAtDB is available now. This
network version uses the same powerful query facility that is built into
the ACeDB software but the user interface is still in its infancy.
If you wish to obtain the AAtDB database look for our following message.
The message will describe in more detail the database system
requirements, network retrieval procedures for obtaining the database
and methods of obtaining future updates.
For more information contact Mike Cherry or Sam Cartinhour at FAX number
617-726-6893 or via electronic mail at curator at frodo.mgh.harvard.edu.
Sam Cartinhour, J. Michael Cherry and Howard M. Goodman
Department of Molecular Biology, Massachusetts General Hospital
Department of Genetics, Harvard Medical School
Susan McCarthy, Doug Bigwood and Steve Heller
United Stated Department of Agriculture
National Agricultural Library and Agricultural Research Service
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