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Arabidopsis cDNA Analyses on the Web

Ernest Retzel ernest at lenti.med.umn.edu
Sat Sep 9 08:43:45 EST 1995


   **WWW Access to Analytical Information on Plant EST Projects**


           Sponsored by the National Science Foundation

                   Computational Biology Centers
                          Medical School
                      University of Minnesota
                        Minneapolis, MN USA
                 The DOE Plant Research Laboratory
                      Michigan State University
                        East Lansing, MI USA

The Arabidopsis cDNA Sequencing and Informatics Projects are pleased to
announce a WWW server which provides access to analytical information
related to the cDNA clones.  The sequencing and information processing
are joint projects of the DOE Plant Research Lab at Michigan State
University, the Computational Biology Centers of the Medical School
and the Department of Computer Science at the University of Minnesota.
Both projects are sponsored by major grants from the National Science

The server has been in a testing and improvement mode, but available to
the community for approximately one year.  At this site, we provide
analytical information about the >15,000 Expressed Sequence Tag (EST)
sequences that have been produced from clones from the lambda-PRL2 cDNA
library from Arabidopsis thaliana var. Columbia.  This library, as well
as the individual clones from this project, are available at the Ohio
State Stock Center. Complete analytical information is also included on
the French Arabidopsis cDNA sequences, which are also available through
the stock center.

The specific information stored on this server includes the full BLAST
results, the results of screening for low compositional complexity
regions, and the LC-masked results of BLASTP.  The primary access to
the multiple gigabytes of data is via a WAIS index of these results,
such that a key word search, or query, can be made against the server,
and all hits to that query can be seen.  In this fashion, you can use
this server to find information relating to the clones that have thus
far been sequenced, analyzed and deposited in dbEST.  For example, if
your work involved cellulase, you might be interested in all clones
which have been sequenced which are similar to other cellulase
sequences in the database, and would find several hits to this

In addition to the Arabidopsis sequences, there are also some 4,000
results from the Rice Genome Project [soon to be 10,000+], 1,100+
sequences from maize and 200+ from loblolly pine.  You may conduct your
searches using an individual genome or any combination of genomes.
The sequences are provided via direct collaborations with some of the
researchers, or are extracted, in some cases, from dbEST.

A tutorial, which has been published in Weeds World, the international
electronic Arabidopsis research journal, explains the server content in
detail.  The article is the first one in the Informatics section of Vol
2(ii), and it can be found in the journal's table of contents at
[http://nasc.life.nott.ac.uk:8300/Vol2ii/contents.html]. The full
content of the Plant Molecular Information Center [PMIC] server and its
capabilities and future is too extensive for an announcement of this
nature, but is detailed in this article.  In addition to the blast
results, the article describes many tools attached or about to be
attached to the server, and references several full-length articles
about the development of the server (these articles are also available,
with full text and graphics, on the Minnesota server).

The server is available via Mosaic or NetScape at [http://lenti.med.umn.edu].
Click into the first item under "Research Projects".  When you visit
our site, *please be sure to register as a user*; this will insure that
you are notified directly when we add to the server with additional
sequences and software [a relatively frequent event in both cases].

Ernie Retzel, Computational Biology Centers, Medical School,
     University of Minnesota
        ernest at lenti.med.umn.edu

Tom Newman, DOE Plant Research Laboratory, Michigan State University
        22313tcn at msu.edu

And members of the Sequence Database Team at the University of Minnesota:

Kristi Swope, Ph.D. [Dept. of Computer Science and Plant Molecular Information
Paul Bieganski, Ph.D. [Dept. of Computer Science and Plant Molecular
     Information Center]
Elizabeth Shoop [Dept. of Computer Science]
Ed Chi [Dept. of Computer Science]
Olaf Holt [Dept of Computer Science]

And from the Dept. of Computer Science:
John V. Carlis, Ph.D.
John Riedl, Ph.D.
Phillip Barry, Ph.D.

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