New Blast Form at AtDB

Eva Huala huala at genome.stanford.edu
Mon Aug 2 17:53:57 EST 1999


   AtDB is pleased to announce a new version of our BLAST form at:

  http://genome-www2.stanford.edu/cgi-bin/AtDB/nph-blast2atdb

The new version has two new features: results returned by email and
the ability to upload the query sequence from a text file.  The
sequence, as with all searches, is not logged or stored.

We have also placed an upper limit of 2000 amino acids on the query
sequence for TBLASTN and 2000 nucleotides for TBLASTX.  These limits
do not apply if the email results option is selected or if the New
and Recently Changed dataset is chosen for searching.  There are no
limits on BLASTN, BLASTP, and BLASTX.

To use the email option:

1) Enter your email address in the EMAIL Return Option box
2) Select a format (URL, HTML Format, or Text Output)
If you choose a URL, an email message will be sent to you containing
a URL at which you can view your results.  For the other two options,
the results will be in an email message in the format you chose.

To use the Upload Local File option:

Macintosh:
1) Click on the Browse button
2) Click on folders to open them, and on the file to upload it

PC:
1) Click on the Browse button
2) Change the file type from "HTML" to "all files"
3) Click on folders to open them, and on the file to upload it

UNIX:
1) Click on the Browse button
2) Change *.html to * at the end of the string in the Filter box
3) Click on a folder and then the Filter button to open the folder
4) Click on a file and then the OK button to upload it

Notes on the format for the file to be uploaded:
-It can be FASTA, GCG, or raw text.
-To use a Microsoft Word file, first save it as plain text.

To search with very short (less than 30 nt) sequences, reduce the
S value before starting your search.  If the S value is too high,
even a perfect match to your sequence will not be reported.  As a
rough guide, use an S value no more than 4 times as large as your
sequence length.

AtDB's Homepage: http://genome-www.stanford.edu/Arabidopsis/

Please send comments to atdb-curator at genome.stanford.edu

Eva Huala
AtDB Curator




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