Proposed posting of new & updated Arab. sequences

David Flanders flanders at GENOME.STANFORD.EDU
Mon Feb 12 15:32:38 EST 1996


The Arabidopsis thaliana Database (AtDB) project at Stanford
University would like your feedback on the following:

We propose to post to this newsgroup, three-times a week, an
automatically-generated list of new Arabidopsis DNA sequences in
GenBank.  This will also include any GenBank Arabidopsis entry with an
updated sequence, but will exclude those entries with changes only to
the sequence annotation or references.

An example of such a sequence posting (for 10 Feb.) is given below.

Lists will not include the many EST DNA sequences that are deposited
to the DNA databases.  We are only processing new sequences provided
by the NCBI's GenBank. (An international collaboration between the
NCBI, EBI, NCGR, and DDBJ, means that any sequence deposited in one of
these databases will be available from them all.) If no new sequences
are found for any particular period, no message will be sent.

If you have strong feelings either for or against such postings,
please e-mail me with your opinions, using "Sequence Survey" as the
Subject to:

	atdb-curator at genome.stanford.edu

The overall nature of the response will determine whether the
posting-service is implemented.  

The processing of the GenBank sequences will occur, however, whether
the postings are sent to the Arabidopsis newsgroup or not. This is
because we process DNA and protein sequence databases as part of WWW
BLAST and FASTA search for only Arabidopsis sequences provided by
AtDB.

It may be relevant to note that the Saccharomyces Genome Database
(SGD) project, which like AtDB, is one of the Stanford Genomic
Resources, has been successfully providing a similar service for over
a year to the yeast community through their BioSci newsgroup.

David Flanders
AtDB Curator


Example Arabidopsis sequence posting:
--------------------------------------------------------------------
 
New Arabidopsis Sequences 02/10/96

ATGSHII     X83411     1620bp    RNA      PLN      15-JAN-1996
    A.thaliana mRNA for glutathione synthetase.
    glutathione synthetase; GSHII gene; GSH2.

ATHSEQB     M80567     1964bp    DNA      PLN      05-FEB-1996
    A.thaliana non-specific lipid transfer protein (LTP1) gene, partial cds.
    lipid transfer protein; LTP; secretory protein; epidermis; signal
     sequence; LTP1; non-specific lipid transfer protein.

ATKAT1VG    X93022     2304bp    RNA      PLN      22-JAN-1996
    A.thaliana mRNA for voltage gated potassium ion channel.
    K+ channel; kat1 gene; kat1.

ATU04876    U04876     1921bp    mRNA     PLN      19-JAN-1996
    Arabidopsis thaliana Columbia myo-inositol-1-phosphate synthase mRNA,
     complete cds.
    myo-inositol-1-phosphate synthase.

To obtain any Arabidopsis DNA sequence use the NCBI retrieve e-mail
server, retrieve at ncbi.nlm.nih.gov - send the word help and
instructions will be returned.

World Wide Web servers to obtain sequences are:
 NCBI:   http://www.ncbi.nlm.nih.gov/Search/
 EBI:    http://www.ebi.ac.uk/ebi_docs/embl_db/ebi/topembl.html
 GSDB:   http://www.ncgr.org/gsdb/
 DDBJ:   http://www.nig.ac.jp/

BLAST & FASTA searches of only Arabidopsis Sequences are available from:
  http://genome-www.stanford.edu/Arabidopsis/

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