yeast database and map positions

Mike Cherry cherry at GENOME.STANFORD.EDU
Wed Feb 1 12:05:50 EST 1995


I was asked the following question via e-mail and thought the answer
would be appropriate for this group.

Michael Lichten asked via e-mail:
> I want to construct a comparison of the physical and genetic maps of
> chromsomes III and VIII.  What's the easiest way to download the
> ENTIRE set of genetic distances from the database?  The physical bit
> isn't a problem.

The short answer is that you can get this from the SacchDB database on
a Macintosh or UNIX computer using the Query or TableMaker options.  I
have already created several tables as mentioned below.  This sounds
like it might be generally useful so I created the table with the
TableMaker and put it on the Gopher and ftp in a directory called
map_comparison, see below for the address.  I should point out that
the physically mapped objects have a length, there is a start bp and
an ending bp.  Also for an odd reason the table contains the bp /100.

URL to Map comparison tab-deliminated text file:
gopher://genome-gopher.stanford.edu:70/11/Saccharomyces/tables/map_comparison

The longer answer: It is straight forward to get a list of all loci
that have been both genetically and physically mapped if you are using
the Macintosh or UNIX version of SacchDB.  Select the Query option
from the main window and enter:

   >?Locus Map AND Positive_clone

However, the physical map position (bp) is provided from the Clone
object. This is easy to put into a table using the ACEDB TableMaker
option, I can send you the TableMaker definition if you are
interested. Some examples of using the TableMaker are provided with
the release.

You can do the first type of query with the WWW interface by clicking
on "Use the Query Builder or Query by examples to construct a complex
query".  Then click on Locus Query.  Now in the form put a * in the
Map field and also in the Positive_clone field.  Click on Search and
the resulting list should be all loci on the genetic and physical map.
Unfortunately at this time you can not dump this result into a file
via WWW.  The TableMaker is not accessible from WWW.

Another method, where the information is present but spread across
different files, is using a set of tables that I have prepared.  There
are Excel documents and tab-deliminated text files and they are
available via anonymous ftp and Gopher.  For WWW the URL would be:

  gopher://genome-gopher.stanford.edu:70/11/Saccharomyces/tables

There are two tables: "Genetic Map" which contains all genetically
defined genes and "Physical Map" all physically mapped genes.  A
cleaver person with Excel can obtain the set of genetically and
physically mapped genes.  You still need the physical map location,
some of which are in the table "ORF Locations" which has all the ORFs
from the seven sequenced chromosomes.  I can add more tables to the
server as needed.  The Macintosh or UNIX versions of SacchDB are all I
am using to create these tables.

MIke

---
J. Michael Cherry                       Internet: cherry at genome.stanford.edu
Stanford DNA Sequence & Tech. Center    Saccharomyces Genome Database
Stanford University School of Medicine  Stanford, California  94305-5120
Voice: 415-723-7541                     FAX: 415-723-7016

     Contacts for the Saccharomyces Genome Database Project (SGD)
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