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Announcing TIGR's Arabidopsis Database for EST Assemblies

Steve Rounsley rounsley at TIGR.ORG
Tue Mar 12 17:18:38 EST 1996


To all Arabidopsis researchers,

I am pleased to announce the first full release of TIGR's Arabidopsis
database which is available on the WWW at the following URL:

                http://www.tigr.org/tdb/at/at.html

The database contains the same Arabidopsis EST sequences available at dbEST
and at the University of Minnesota, but in a slightly different form.  We
have grouped overlapping EST sequences into contigs, or 'assemblies'.
These assemblies can generally be thought of as containing ESTs that are
derived from the same gene, and therefore help reduce redundancy in the
data.  For instance of the nearly 24,000 sequences in this release of the
database, 15,200 were part of only 3,764 assemblies.  The remaining 8,700
sequences did not group together.

The database contains both individual ESTs and the consensus sequences of
each assembly along with details of which ESTs are contained within the
assembly.  Each consensus sequence has been searched against the public
databases and the most significant match used to assign a putative
identification.

Searching of TIGR's database can be performed in three ways.
 - The putative identifications can be queried in a plain text search.
 - The sequences of ESTs and assemblies can be searched with either a
nucleotide or amino acid query.
 - The details of a given EST can be retrieved using its accession number.

The information in our database is designed to complement other resources
available on the WWW, and we are working to ensure interconnectivity
between the Arabidopsis cDNA database at the University of Minnesota, and
the Stock Center at Ohio State University.  For each sequence, links are
available to the Genbank record, and to the wealth of information available
at the University of Minnesota.  Hopefully the information available in
TIGR's database in combination with the already existing resources will
enable researchers to get the most out of the valuable EST data that has
been produced by Tom Newman and others.

For any users who have been using the database prior to today, the main
difference you will notice is that putative identifications have now been
assigned to all assemblies that have significant matches. Previously, all
the sequences were present, but many were still nameless as they had not
been searched against the databases.

If you have any questions regarding our database, please feel free to
contact us at  at at tigr.org

__________________________________
Steve Rounsley
The Institute for Genomic Research
9712 Medical Center Drive
Rockville, MD  20850





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