AtDB WWW searches of Arabidopsis sequences

David Flanders flanders at GENOME.STANFORD.EDU
Thu Feb 1 12:59:19 EST 1996


DATABASE SEARCHING AGAINST DATABASES OF ONLY ARABIDOPSIS SEQUENCES

The Arabidopsis thaliana Database (AtDB) project at Stanford
University formally announces the availability of BLAST and FASTA
searches via the World Wide Web (WWW).  These searches are performed
on Arabidopsis DNA or protein sequences exclusively.  The DNA-sequence
data-set comprises all Arabidopsis sequence contained within GenBank,
including ESTs.  The protein data-set is a non-redundant database of
Arabidopsis protein sequences.  This is prepared by processing the
open-reading-frame translations present in GenBank, known as the
GenPept dataset from NCBI, as well as the SwissProt and PIR protein
databases.  All Arabidopsis protein sequences from these three
databases are combined.  Sequences found to be identical at the
amino-acid level are merged.

Arabidopsis searching using the BLAST and FASTA programs is available
via the WWW from the URL:

	http://genome-www.stanford.edu/Arabidopsis

Look for the "BLAST Searches from AtDB" or "FASTA Searches from AtDB"
links.

The Arabidopsis non-redundant protein-database can be retrieved in
FASTA format for use on your computer via Anonymous FTP from:

 ftp://genome-ftp.stanford.edu/arabidopsis/At_Protein/at_nrpep.fasta

The Arabidopsis GenBank and non-redundant protein-databases are
updated three times a week.

The WWW forms allow several options to be changed for both BLAST and
FASTA searches.  The results of the searches are presented with WWW
links to GenBank, GenPept, EMBL, SwissProt, and PIR/MIPS.

Please send any comments or questions regarding BLAST and FASTA
searches from AtDB using the SUGGESTIONS... form on AtDB or by
e-mailing to:

	atdb-curator at genome.stanford.edu





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