AAtDB release 1-5
Release 1-5 of AAtDB, An Arabidopsis thaliana Database, is now
available for Unix workstations as well as through the Internet using
the Gopher and WAIS software clients.
This release of AAtDB includes several new and updated types of
o New and revised stock information provided by Mary Anderson of the
Nottingham Arabidopsis Stock Centre.
o Over one hundred new images of Arabidopsis ecotypes and mutations
available from either the Ohio State or Nottingham stock centers.
o Over one thousand new DNA sequences from GenBank including the
sequence similarity of these sequences to entries in the protein
sequence databases as defined by NCBI's BLASTX software.
o Several new and updated Colleague entries.
o New bibliographic information from Medline.
AAtDB Class Sizes in release 1-5:
Class Name Total Entries New Entries in 1-4
=============== ================= ====================
Allele 293 165
Author 4272 243
Chromosome 25 0
Clone 14606 0
Clone_Grid 2 0
Colleague 1277 15
Contig 1196 0
DNA 2485 1066
Gene_Class 243 2
Gene_Product 187 40
Image 235 113
Journal 361 8
KeySet 22 4
Keyword 5369 256
Locus 1398 143
Paper 3535 187
Phenotype 1449 54
Population 26 6
Probe 426 1
Restriction 338 0
Sequence 9006 4097
Source 58 1
Strain 5567 1081
2_point_data 3741 0
AAtDB uses the ACEDB software developed by Richard Durbin (MRC-LMB,
U.K.) and Jean Thierry-Mieg (CNRS, France). The AAtDB project is
funded by the U.S. Department of Agriculture Plant Genome Research
Program through the National Agricultural Library. The AAtDB project
is staffed by members of the Department of Molecular Biology at
Massachusetts General Hospital and Harvard Medical School, Boston USA.
AAtDB is available without charge via Internet FTP transfer and remote
X-windows access (see below).
AAtDB features a wide variety of public information that is presented
using graphical, text, and tabular formats. The user interface, which
was designed to invite browsing, allows users to explore information
by pointing and clicking with the workstation mouse or by using a
versatile query facility. ACEDB allows all parts of the database to be
cross-referenced with each other. The large number of interconnections
provides a dense navigable network in which information can be located
from many different starting points (see sample screen in appendix).
All information contained within AAtDB was obtained directly from the
original authors or from publicly available collections and databases.
Updates to AAtDB are periodically distributed and the database is now
in its fifth data release. A partial list of the information AAtDB 1-5
-- The Hauge/Goodman cosmid physical map including greater than 14,000
cosmid clones. The contigs of the physical map are associated with the
-- Genetic markers, including RFLP, RAPD, and "classical" markers.
-- Genetic maps, including the Integrated map from Hauge et al. (1993)
The Plant Journal, a visible marker map including many embryo
defective loci from David Meinke, and RAPD maps from Scolnik et al.
-- Primary F2 and RI population recombination data from the Goodman,
Meyerowitz, Scolnik, and Dean laboratories.
-- Primary 2-point data from M. Koorneef, D. Meinke, and others.
-- Strain list, now maintained and entered for AAtDB by Mary Anderson
at the Nottingham Arabidopsis Stock Centre. Includes many new entries
from the Nottingham and Ohio State stock centers.
-- List of Arabidopsis researchers, including postal mail address,
telephone and FAX numbers, electronic mail address, publications,
research interests, and research associates. Information on over 1200
colleagues is included.
-- All Arabidopsis DNA sequences from GenBank and EMBL DNA sequence
databases as well as the EST (expressed sequence tags, i.e., cDNA)
reports from the NCBI's dbEST database on the MSU and French
sequencing efforts, with over 2400 entries total.
-- NCBI BLASTX (six frame translations searched against the NCBI
non-redundant peptide database) defined peptide sequence homologies
for all DNA sequences included in AAtDB.
-- Phenotype descriptions from the Green Book by Meyerowitz and
Pruitt, updated with descriptions from the Nottingham and Ohio State
-- Scanned images of RFLP autoradiograms from the Goodman lab,
photographs of mutant plants from G. Redei and M. Anderson, and
ethidum bromide-stained restriction enzyme digests of RFLP probes
distributed by the ABRC.
-- Bibliographic citations, including references for all articles from
the Arabidopsis Information Service, currently numbering 3400.
AAtDB 1-5 utilitzes the new ACEDB 1.10 software providing fixes and
new features. Note that the ACEDB software is now available for the
public Unix version called Linux that runs on Intel 386 and 486 based
systems! For more information about Linux retrieve the linux.readme
file via anonymous ftp or Gopher.
The ACEDB software is developed by Richard Durbin (MRC-LMB, Cambridge,
UK) and Jean Thierry-Mieg (CNRS, Montpellier, France). Precompiled
executables of ACEDB are available for Sun SPARC (SunOS and Solaris),
DEC MIPS and Alpha, NeXT, IBM-6000, and Silicon Graphics workstations
under the X-windows environment plus Intel 386 and 486 computers
running Linux. ACEDB can be compiled on Suns under Sunview or Sun386i
under OpenWindows, Alliant, and CONVEX computers. A Macintosh version
is in development.
All the AAtDB information in text form is available via the
Arabidopsis Research Companion, an Internet Gopher server available
from the host Weeds.MGH.Harvard.EDU. For convenience the bibliographic
references have been converted to Macintosh EndNote and the general
bibliographic format called refer. The new images obtained from the
ABRC at Ohio State University are available as GIF files. All these
files are available via Gopher and anonymous ftp from the host
Weeds.MGH.Harvard.EDU (IP 22.214.171.124).
Using Gopher to search AAtDB and retrieve information:
Internet Gopher was developed by the University of Minnesota. It
requires a computer that is connected to the worldwide Internet
network. Software referred to as a Gopher client is available for most
types of computer, most of these are available via anonymous ftp from
If your computer manager cannot provide you with one of the free
Gopher clients but you have access to telnet you can use a public
access account provided by the Department of Molecular Biology at
Massachusetts General Hospital. Simply telnet to the host
Weeds.MGH.Harvard.EDU (IP 126.96.36.199), use the username gopher,
there is no password. A Gopher client will start that automatically
connects with the AAtDB Research Companion. Text information can be
mailed from the public gopher account by using the "m" option.
However the images cannot be viewed using the public telnet account.
A Gopher client on your local computer is required to view images, or
you can transfer the images via an ftp or Gopher client to an
intermediate computer subsequently transferring the image to a
workstation or personal computer that can display GIF and JPEG images.
Remote Access to the Unix AAtDB database using X-windows
Remote access to the full Unix version of AAtDB is now available to
computers with a good Internet network connection and X-windows
software. This means that most Unix workstations using OpenWindows,
Motif, or any of a large number of other windowing environments based
on MIT's X-windows can access a remote server that will display the
graphic interface of AAtDB on the local computer's display. For
personal computers a variety of commercial X-windows emulation
software is available: Macintosh users can purchase eXodus (White Pine
Software) or MacX (Apple Computer), MS Windows users can use Vista
eXceed plus (Hummingbird Communications) or DESQview/X (Quarterdeck
The basic procedure is to login on the host weeds.mgh.harvard.edu
using the username 'aatdb'; no password is required. If you are on a
Unix X-windows workstation you will need to issue the following
command before connecting with the server:
% xhost weeds.mgh.harvard.edu
The above command is required to allow the AAtDB server to create and
display windows on your computer. After login you will be asked two
questions about your computer: (1) do you have a color monitor, and
(2) do you need to change the hostname. If you are using an
X-terminal, a special device that displays X-windows graphics, you
will need to change the hostname to the hostname of the X-terminal.
If your computer has a color monitor and is not an X-terminal you can
use the login name "c-aatdb". This login name is also useful for some
of the X-windows software on personal computers.
How to obtain the Unix version of AAtDB:
Detailed information about how to retrieve the Unix update information
are included in the file AAtDB.Retrieval_Installation on the
Weeds.MGH.Harvard.EDU (in the aatdb directory) and NCBI.NLM.NIH.GOV
(in the repository/aatdb directory) via anonymous ftp. You can also
obtain this file via our Gopher from the "AAtDB FTP Archive" folder.
Please send submissions of new information (mapping and colleague
listing or any of the other types of information provided) to the
AAtDB Project via electronic mail at curator at Frodo.MGH.Harvard.EDU or
via FAX at 617-726-6893. Please help us make this resource better by
providing some of your data and information.
Special thanks to all those that many submitted information.
This will be the last release produced by the team of Sam Cartinhour
and Mike Cherry. The AAtDB Project is now in being turned over to
John Morris who starts on September 15th.
For more information about the AAtDB project please contact John
Morris at FAX number 617-726-6893 or via electronic mail at
curator at frodo.mgh.harvard.edu. By postal mail contact John Morris,
Department of Molecular Biology, Massachusetts General Hospital,
Boston, MA 02114, USA. A printed tutorial manual "An Introduction to
ACeDB: For AAtDB--An Arabidopsis thaliana database" is available on
request from the AAtDB project.
J. Michael Cherry, Sam W. Cartinhour and Howard M. Goodman
Department of Molecular Biology
Massachusetts General Hosp