Full Genome Searches from SGD

Mike Cherry cherry at GENOME.STANFORD.EDU
Tue Apr 30 10:17:09 EST 1996

I'm sorry if you have seen this message before, this is the third time
I've sent it.  None of the previous attempts have been seen in the
newsgroup or mailing list at Stanford.


Congratulations to the hundreds of individuals that were involved in
determining the complete genomic sequence of yeast, and to the
thousands of researchers that can now ponder the first sequenced
eukaryotic genome.

The Saccharomyces Genome Database (SGD) is mirroring the sequence and
reference files released by MIPS on April 24th.  We will also be
watching for the completed annotations and will mirror them as well.

SGD is providing BLAST and FASTA searches against the complete genomic
sequence via the WWW.  I have placed limits on the maximum number of
simultaneous searches.  Thus if while attempting to start a search you
receive a message that our server is too busy please try again in a
few minutes.  Also to help minimize the load on our computer and allow
others to run a search please use short sequences as your query.  A
TBLASTN search performed with the full length sequence of a large gene
can take 10 minutes of CPU time to complete.  Most searches of a few
hundred amino acids require a couple minutes of CPU time. BLASTN and
BLASTP are much quicker.

To perform a search against the complete Saccharomyces genome go to
the SGD home page and follow the links labelled BLAST or FASTA.


SGD is also providing a WWW form to allow any arbitrary region of the
complete sequence to be retrieved.  This form is available from all
the BLAST and FASTA results pages and from the "Chromosomes" link on
most SGD pages.

SGD is currently working to integrate the newly released sequence into
its database.


J. Michael Cherry                       Internet: cherry at genome.stanford.edu
Department of Genetics                  Stanford University School of Medicine
Medical Center, Room M311               Stanford, California  94305-5120
Voice: 415-723-7541                     FAX: 415-723-7016

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