Updated BLAST & FASTA Searching from AtDB

Mike Cherry cherry at genome.Stanford.EDU
Sat May 17 11:20:29 EST 1997


The searching software on the AtDB Web server has been updated.

For BLAST searches the new BLAST2 from Warren Gish at Washington
University is now available.  This new version of BLAST provides all
the old features plus gapped alignments.  The gapping is turned off by
default, to turn it on look for the "Output format" option and select
"gapped alignments".

For FASTA searches the FASTA3 version t77 from Bill Pearson at
University of Virginia is online.  You can now select from FASTA,
FASTX, or TFASTA searches.

Two data sets are available for both BLAST and FASTA searching.  All
Arabidopsis sequences contained within any part of GenBank, and a
non-redundant protein data set produced by AtDB from SwissProt, PIR,
and GenPept.  These data sets are also available from the AtDB FTP
server.

Links to the BLAST and FASTA forms can be found at the top of the AtDB
home page:
               http://genome-www.stanford.edu/Arabidopsis/

Mike

P.S. The preliminary sequences from the Davis & Federspiel
(http://sequence-www.stanford.edu/ara/Arabidopsis) project can also be
searched from AtDB's Web server.  The preliminary sequences are
periodically updated and then removed once the sequence is submitted
to GenBank.  The URL for these preliminary sequences is:

   http://genome-www2.stanford.edu/cgi-bin/nph-blastprelim






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