gene mapping databases

[Mark Johnston]

Dear buddies,

        We are writing to remind you of the existence of a database
that contains the locations of all the Riles-Olson lambda clones of
the yeast genome, and the locations of many genes that have been
mapped to those clones.  We want to encourage the yeast community to
make a New Year's resolution to use the Riles-Olson filters to map
your genes, and, _MOST IMPORTANTLY_, to ENTER THE MAP LOCATIONS OF
YOUR GENES INTO THE DATABASE in order to keep it current and ensure
that its utility to the yeast community is maximized.  (Entering the
data is accomplished by submission to Yeast Genome Database, as
described below).

        As many of you know, the Riles-Olson physical map of the yeast
genome (Genetics 134:81) has proven very useful for mapping and
cloning (Genetics 134:151) genes.  In the past, Linda Riles has
provided filters of the lambda "prime clones" that comprise the map,
and has interpreted the results of hybridizations of cloned genes.
Because of the large number of people that are mapping their cloned
genes using the filters, Linda can no longer provide this service.
Fortunately, Mike Cherry of Stanford has made the Riles-Olson database
available over the Internet (see description below), as part of his
efforts with David Botstein to establish a public yeast database.
However, we are concerned that when someone determines the map
location of their gene using this database, this information is not
getting entered into the database.

        In our opinion, this severely limits the usefulness of the map
and the database.  We believe the major purpose of the database is to
alert people to the fact that they may be studying a gene that is also
being analyzed by others.  Oftentimes, making this connection can
provide both workers with clues to the function of the gene, and
thereby accelerate our understanding of how our favorite organism
functions.  Obviously, the more complete and up-to-date the database
is, the greater are the chances that it will prove useful in this way.
        
        The yeast community is an exceedingly cooperative group, so we
are optimistic that people will provide this information publicly, if
they know how to communicate it.

ONCE YOU LOCATE YOUR GENE using the Riles-Olson filters and the
database on the Internet (see below for instructions), you can SUBMIT
THIS INFORMATION BY SENDING A MESSAGE TO:

               yeast-curator at genome.stanford.edu

or by FAXing the information directly to:

               Yeast Database Curator, FAX: 415-723-7016 

Please include the gene/clone association, a very brief description of
how the association was determined, and any comments you wish to be
included.  All submissions will be immediately added to the
information available via Gopher.  A complete Yeast Genome Database is
under development at Stanford and will be available later this year.
This database will include methods useful for submitting a variety of
yeast genome information.

        Below we have appended Linda Riles' last "Filter Users News"
that describes how to access the database and where to obtain the
"prime clone" filters.  We would like to thank Mike Cherry and Linda Riles
for their considerable efforts in making this resource available.   We urge
everyone to take advantage of this resource  and to encourage your
colleagues who may not know how to use it to join in the cooperative
efforts of our community to help "figure
out how yeast works."

Sincerely,

                Mark Johnston           mj at sequencer.wustl.edu
                Phil Hieter                  Phil_Hieter at qmail.bs.jhu.edu 





September 1993
FILTER USERS' NEWS

        This is the sixth and last in a series of newsletters for labs
that are using prime clone grid filters to map new genes. Until
recently, I have interpreted results of prime clone grid filter
hybridizations and have notified filter users of the map locations of
their newly cloned genes.  Since the yeast physical map is now nearly
complete, I am starting new projects and will no longer provide this
service.  Mike Cherry from David Botstein's group at Stanford is
constructing a yeast genome database with funding from the NCHGR/NIH.
Because the Stanford Yeast Genome Database now includes our data, my
involvement is no longer necessary.  In addition, last summer I sent
filter users a paper data base that enables you to locate newly cloned
genes in most cases.  If you did not receive the paper database, send
me your current postal address on a mailing label, and I will send
another.  Please share it with other members of the yeast community.

          People using prime clone grid filters can submit new gene
locations to the Stanford database, as well as find out what genes
have been located in clones of interest.  The yeast database at
Stanford is accessible through Internet Gopher software (see attached
protocol).  To submit information or to ask a question send a message
to:                                                                           
                yeast-curator at genome.stanford.edu

        Our (Washington University) database, much of which is
included in the database at Stanford contains over 600 genes from 175
labs.  The locations of sixty of these genes have been entered in the
Stanford database.  We strongly encourage you to submit the remaining
ones you may have in order to make the information at Stanford as
useful as possible for the yeast community.

        Prime clone filters are available from the ATCC at $250 a set.
Protocols and much information from the database are provided with the
filters.  A new updated catalogue will be available in the fall.

        Filters:  Catalogue #77284      call   800-638-6597

The ATCC also provides the Olson lambda and cosmid clones.  Lambda
clones can be converted to plasmids for complementation testing when
the map location of the gene of interest is known (see Erickson and
Johnston, 1993. Genetics 134: 151-157).  An analogous vector for
converting cosmids into plasmids will be available soon.

         1-24 clones    $55/clone               (USE OUR C600 HOST FOR
        25-75 clones    $30/clone               LAMBDA CLONES:   #47048)
          >75 clones    call ATCC

BIO101 is also selling filters and clones at prices competitive with
the ATCC.  Call Richard Dana at 800-424-6101.

                                                Sincerely,
                                                Linda Riles

                                                                           
STANFORD YEAST GENOME DATABASE

        An early version of the yeast database is available via
Internet Gopher, which provides access to different types of
information from locations around the world.  Gopher software provides
topics in a simple hierarchy of menus.  Items in Gopher menus can
represent a number of services, including anonymous FTP and WAIS
servers, and text, binary, Macintosh, DOS or PostScript files.  These
services can be provided either by the computer being used for the
Gopher server, or by other computers.

        Internet Gopher clients are available for many computer types
and require that the computer is connected directly to the Internet.
A modem connection is not sufficient.  One of the better Gopher
clients for the Macintosh is TurboGopher.

        ***If you have a Gopher client on your local Internet
connected to a Unix or VMS system, you can reach our service with the
command:
                  gopher genome-gopher.stanford.edu

        ***If you have TurboGopher on your Mac, double click on its
icon, choose the option "Another Gopher" under the file menu and enter
hostname:
                  genome-gopher.stanford.edu

Direct questions about access via Gopher and about information
available from the Yeast Genome Database to:

                  yeast-curator at genome.stanford.edu
                                                                           
        You can access physical maps containing Washington University
clones available from the ATCC with the Stanford Gopher server.  First
select the folder "Saccharomyces Information" and then choose the menu
item:
                   Saccharomyces Genome <?>

        Queries can include gene symbols, ATCC clone numbers or
Washington University clone numbers.  The wild card '*' can be used at
the end of a word, but not at the beginning.  For more information on
searching see Help Searching the "<?>" database on the Gopher menu.

        The database group requests your suggestions on how to make
this resource more useful for your work.  It will send announcements
to the BioSci Yeast mailing list as new resources become available.
Subscribe by sending an e-mail message to biosci-server at net.bio.net
and simply include the following line in your message:

                    subscribe yeast

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        Mark Johnston
        Department of Genetics Box 8232
        Washington University Medical School
        4566 Scott Ave.
        St. Louis, MO  63110
        FAX:   314-362-2985
        TEL:    314-362-2735
        E-mail:  mj at sequencer.wustl.edu