a yeast genome database

Mike Cherry cherry at cycle.Stanford.EDU
Wed Sep 8 12:01:15 EST 1993


Just a brief note today. We are building a yeast genome database at
Stanford supported by NCHGR that will be a public resource. There will
be announcements very soon about version 0.1 of the database which
will be accessible via gopher, anonymous ftp and World Wide Wed.
We'll have Olson's physical map, Mortimer's genetic info, and pointers
to sequences. However this is just the beginning. We are putting
together a database built on an object-oriented model that will be
accessible via the Internet. Currently we are hoping to support
several different clients that will be available on almost all types
of computers. Different clients will be available to hopefully match
the needs and computer resources of our diverse community. The
database will provide all types of genome information and as much as
possible links of other databases. There will be more announcements in
the coming months as this systems goes online.

For those that need access to the physical map of the clones available
from the ATCC you can currently look to our Gopher server, lets call
this version 0.0 of the database. Please note that this server will be
moving to a new computer that is on order and due any day. Thus we
might be down for a day or two in the near future. So consider this a
prerelease announcement, this means we are not yet in production mode.

You can use gopher to connect with genome-gopher.stanford.edu to
access the very prerelease yeast database. Look for the menu item:
"Saccharomyces Genome <?>". This is a WAIS search index that contains
information from LISTA2 with the addition of the sequence description,
text pictures of the Washington University clones available from ATCC,
plus some additional information about association of some loci to the
physical map. Queries can include for gene symbols, ATCC clone
numbers, or WashU clone numbers. The search modifiers 'and' plus 'not'
and available, 'or' is assumed. The wildcard '*' can also be used at
the end of a search word, sorry but you can not use it at the
beginning of a word.  A simple example follows, for more information
on searching see the "Help Searching the "<?>" database." on the
Gopher menu.

Select the "Saccharomyces Genome <?>" item, you will be asked for
"Words to search for". Enter:   adh*

You will see something like:

 -->  1.  Gene Name  (LISTA) : ADH3.
      2.  Gene Name  (LISTA) : ADH4.
      3.  Gene Name  (LISTA) : ADR1.
      4.  Gene Name  (LISTA) : ADC1.
      5.  Gene Name  (LISTA) : ADH1.
      6.  Contig View of ATCC Clone number 70708.
      7.  Contig View of Washington Univ Clone number 6993.
      8.  Contig View of ATCC Clone number 70813.
      9.  Gene Symbol: adh3.
      10. Gene Symbol: adh2.
      11. Gene Symbol: adh1.

Entries 1 to 5 are from LISTA2, entries 6 to 8 are a text view of
the Olson physical map and entries 9 to 11 is information from Linda
Riles about how a gene was located to the physical map.

A partial listing of item 6 is:

Contig View of ATCC Clone number 70708
Washington Univ Clone number 6364
This clone contains adh3; Determined by hybridization
Partial View of Chromosome XIII (size 900631 bp)
Limits of this partial (23.7%) view are: 321147 to 534795
--70823--
 ---70789---
  ------*9532*------
     --70050--
     --71105--
          -----71028-----
                    --71069--
                    -----71044-----
                      --70442--
                           ---70819---
                              ==70708==
                                  --70456--
                                    ---70734---
                                        --70046--
                                          --70697--
                                             --70261--
                                                 --70652--


All this is very experimental. We are very interested in your input on
how we can make this resource more useful for your work. Very soon we
will have much of this information available via anonymous ftp. The
information in the gopher server will also be increasing. The GemStone
network server database with several network clients will hopefully be
available in early 1994.

Mike
-- 
J. Michael Cherry                       Project Manager, Yeast Genome Database
Stanford Genome Sequencing Center,      Department of Genetics
Stanford University School of Medicine, Stanford, CA 94305-5120
Voice: 415-723-7541  FAX: 415-723-7016  Internet: cherry at genome.stanford.edu



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