Mike Cherry 726-5955
CHERRY at FRODO.MGH.HARVARD.EDU
Thu Dec 17 17:04:01 EST 1992
AAtDB 1-3 is now available.
The Unix workstation version is available via anonymous ftp from
weeds.mgh.harvard.edu and ncbi.nlm.nih.gov. The information contained
in AAtDB 1-3 is also available via the Arabidopsis Research Companion
gopher and WAIS service.
The highlights of this release include:
1) Multiple genetic maps. In the previous releases of AAtDB only one
genetic map per chromosome was provided. With this release we include
three genetic maps per chromosome. All of the current maps are
created by the JOINMAP software of Piet Stam (Wageningen, The
Netherlands). The maps differ in the data used as input. Included is
a map of only visible markers, version 1.0 of the Integrated map
currently in press at The Plant Journal, and the map refered to as the
unified map which is the current estimate of the Arabidopsis map. In
the future as the unified map becomes refined it will be promoted to a
new version of the integrated map in AAtDB. David Meinke has agreed
to become the initial genetic map curator and has been involved in the
creation of the visible map in this release.
2) The French Arabidopsis cDNA sequencing effort has recently started
releasing sequences. This release of AAtDB includes 879 cDNA
sequences obtained from the GenBank and EMBL DNA sequence databases.
As with all DNA sequences present in AAtDB the translations of the
cDNA sequences have been compared to PIR, SwissPROT and GenPept
protein databases and the resulting similarities included.
3) Images of autoradiograms representing RFLP "phenotypes"; i.e.,
autoradiograms from experiments in which cosmid probes were used to
detect restriction enzyme polymorphisms on blots of digested genomic
DNAs are also included. Most of the cosmid probes are available from
the ABRC at Ohio State. In this release we include 49 images. These
images are also available via the Gopher server, but not via WAIS. You
can retrieve the image to your computer for viewing. All images are
in the GIF (Graphic Interchange Format) format.
4) Many new strains have been added to the Strain class. The new
entries (currently available only from Nottingham) include color
mutants from the Prof Kranz's AIS collection and recombinant inbred
lines from Caroline Dean and Clare Lister. In addition we now list a
large number of ecotypes from the AIS handbook along with their
characteristics (but most of these are not available yet from either
5) A new class called Phenotype now contains phenotypic descriptions
for individual mutations and for mutant stocks. Many of the phenotypes
associated with stocks have been reviewed by Mary Anderson at the
Nottingham Seed Centre. We are continuing to work with Nottingham to
include the most accurate strain descriptions possible.
6) Bibliographic references and Colleague entries are continually
being updated. The number of bibliographic entries in AAtDB is now
over 2900 and the number of colleague entries is now well over 700.
7) David Meinke's pairwise recombination data is included and used in
the generation of the Visible only and the Unified maps.
8) A new feature in several classes is a list of Hints. The hints are
either an explanation of the specifics about the contents of the
class or an instruction on how to use information in that class. For
example the hints in the image class describe in detail how to view
the autoradiogram pictures via the Unix version of AAtDB.
9) Keysets of new entries. The class Keyset contains lists of new
entries to the 1-3 version of AAtDB. These lists provide a quick
method for you to view just the new entries. For example the 926 new
DNA sequences included with this release are listed in a keyset titled
How to obtain the Unix version of AAtDB
Detailed information about how to retrieve the Unix update file are
included in the file AAtDB.Retrieval_Installation on the
weeds.mgh.harvard.edu and ncbi.nlm.nih.gov via anonymous ftp. You can
also obtain this file via Gopher from the "AAtDB FTP Archive" folder.
The compressed tar archives for this version of AAtDB will be among
several databases available on the next NCBI Repository CD-ROM,
expected in January 1993. Currently this CD-ROM is free; eventually
the NCBI will be releasing two repository CD-ROMs per year via a
subscription service as they currently do for the GenBank and Entrez
CD-ROMs. Orders can be placed via email to
repository at ncbi.nlm.nih.gov or by postal mail to: NCBI Data
Repository; NCBI/NLM/NIH; Building 38A; Bethesda MD 20894.
Please send submissions of new information (mapping and colleague
listing) to the AAtDB Project via electronic mail at
curator at frodo.mgh.harvard.edu or via FAX at 617-726-6893.
Mike Cherry, Sam Cartinhour and Howard M. Goodman
Department of Molecular Biology
Massachusetts General Hospital, Boston, MA 02114 USA
AAtDB is funded by the USDA Plant Research Program through the
National Agricultural Library.
ACEDB software is Copyright (C) 1991 R Durbin and J Thierry-Mieg. All
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