AAtDB 1-5 now available

Mike Cherry CHERRY at FRODO.MGH.HARVARD.EDU
Fri Sep 17 00:03:17 EST 1993


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
information:

  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
contains includes:

-- The Hauge/Goodman cosmid physical map including greater than 14,000
cosmid clones. The contigs of the physical map are associated with the
genetic maps.

-- 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.
(1992) PNAS.

-- 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
stock centers.

-- 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 132.183.190.21).


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
boombox.micro.umn.edu.

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 132.183.190.21), 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
Office Systems).

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 creat



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