[Arabidopsis] PLACE (plant cis-element motif) database: final release

Kenichi Higo via arab-gen%40net.bio.net (by kenchan4311 At yahoo.co.jp)
Thu Feb 1 06:56:57 EST 2007

Please forward this to anyone you think might be interested.

Hello everyone

I am Curator of PLACE (http://www.dna.affrc.go.jp/PLACE/), a database of
nucleotide sequence motifs found in PLAnt Cis-acting regulatory DNA

This message is to inform you that the latest release (PLACE 30.0, 469
entries, Jan.8, 2007) will be the final one. That is, no update of the
data is scheduled in the future, except for the possible correction of
major error(s).

The data collection for this database had been financially supported in
part, from April 1996 to March 2001, by a grant from the Ministry of
Agriculture, Forestry and Fisheries (MAFF) of Japan in the framework of
the Research Project for New Recombinant DNA Techniques. The update of
the database and the improvement of the analysis tools have been carried
out by volunteers, without formal financial support specific for these

I collect motifs and pertinent information by reading articles published
in many journals for plant science, genetics, molecular biology, and
biochemistry, etc. Although abstracts of the most of the papers are now
available free of charge on line, I found reading the Results and
Discussion sections essential to assess accurately the conclusion made
by the authors and to extract important information for the database.

After my departure from NIAS (previously known as NIAR) in March 2005,
it became very difficult to have access to the most of these journals. I
managed to borrow some plant-related journals from an acquaintance who
personally subscribed them, but the subscription was terminated at the
end of 2006. Therefore, to my regret, I decide to terminate the update
of the database.

We will try to maintain the PLACE web site as it is at NIAS for, at
least, a couple of years or, if possible longer. The ftp site for
downloading the data is available now, as before. Anyone interested in
archiving these data are welcome to do so.

I am very grateful to Dr. Y. Ugawa, a database specialist and the
collaborator for PLACE from the beginning, former Head of MAFF DNA
Bank/NIAR, and currently at Miyagi University of Education for his
dedication and continuous encouragement, to Dr. Meena Sakharkar (Nanyang
Technological University, Singapore) for kindly providing us with Web
Signal Scan, and to a group of very talented Bioinformatics and
Information Systems Specialists who have been dispatched to MAFF DNA
Bank from Mitsubishi Space Software Co., LTD. Without their
contribution, the construction, maintenance, updates and improvement of
this database over a span of the past ten years was not possible.

The database server has been, and is now maintained in MAFF DNA Bank at
National Institute of Agrobiological Sciences (NIAS). I am very grateful
to Dr. Y. Nagamura, current Head of MAFF DNA Bank, and his colleagues,
for cooperation.

If you have any question, please send e-mail to:
qxhigok At bank.dna.affrc.go.jp
(This address is also shown at the PLACE web site.)


Kenichi Higo, Ph.D.
Curator of the PLACE database

Ibaraki, Japan

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