yeast database for BLAST

[Mike Cherry]

In article <199608121246.IAA11283 at borduas.nlm.nih.gov>,
 <francis at NCBI.NLM.NIH.GOV> wrote:
>Last week in Madison, a few people told me that it would be convenient
>for them if the new blastable Saccharomyces cerevisiae (yeast) data
>files (in FASTA format) where available for FTP so they could run them
>locally.
>
>We don't have these files updated with any update of the component
>records (at this time), but if people want to use these, we are happy
>to make them available.  They are at:
>
>ftp://ncbi.nlm.nih.gov/blast/db/yeast.nt.Z
>ftp://ncbi.nlm.nih.gov/blast/db/yeast.aa.Z
>
>We do plan to be updating these in the future, on a regular basis.
>

FASTA files containing only yeast sequences are also available from
the Saccharomyces Genome Database (SGD) and have be updated three
times a week (Tue, Thu, Sat) for the past year.  Currently two FASTA
files can be retrieved, these correspond to two of the three data sets
searchable with BLAST and FASTA from the SGD WWW server.

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

All Saccharomyces cerevisiae sequence contained in GenBank, updated
three times a week:

 ftp://genome-ftp.stanford.edu/yeast/yeast_GenBank/yeast_gb.fasta.Z

Non-redundant set of all Saccharomyces cerevisiae protein sequences
from GenPept, PIR, and SwissPROT; updated three times a week:

 ftp://genome-ftp.stanford.edu/yeast/yeast_protein/yeast_nrpep.fasta.Z

A third dataset is available but currently not as a FASTA file.  Its
in the NBRF format used by GCG.  This is the 10Kb overlapping segments
of the entire genome used for the genoSc data set on our BLAST and
FASTA searches.  This data set is updated as changes occur in the
genomic sequence:

 ftp://genome-ftp.stanford.edu/yeast/genome_seq/geno_sc/chrs.seq.Z
 ftp://genome-ftp.stanford.edu/yeast/genome_seq/geno_sc/chrs.ref.Z

Mike
P.S. If there is interest we can provide genoSc as a FASTA file.


J. Michael Cherry                       Internet: cherry at genome.stanford.edu
Department of Genetics                  Stanford University School of Medicine

    Address for the Saccharomyces Genome Database Project (SGD)
             e-mail:    yeast-curator at genome.stanford.edu
          Telephone:    415-725-8956

    General Addresses for Genome Databases at Stanford
                ftp:    genome-ftp.stanford.edu
                WWW:    http://genome-www.stanford.edu/
                FAX:    415-723-7016