AAtDB 1-3

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
stock center).

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
"1-3_New_Sequences".

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
rights reserved.



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