Riles-Olson coordinates

Mike Cherry cherry at genome.Stanford.EDU
Fri Feb 4 12:13:42 EST 1994 

> Dear buddies,
> Does anyone know of an easily accesible source of Riles-Olson fragment sizes? 
> I mean the actual sizes of the R1/H3 fragments that they used for assembling
> their contigs.  I know that such a list exists, because I once got a xerox
> of a page of it from the ATCC.  Such a list is very handy if you are trying
> to determine the orientation of a gene relative to the rest of a chromosome.
> Don't ask why I need to do this--we recombination people do wierd things some-
> times.
> The actual gene I need to orient is THR1, so if anyone out there knows the 
> answer I'll shut up and go away.  But having the fragment size list on the net
> would be nice.....
> 
> Michael Lichten
> lichten at helix.nih.gov

We are working on a method that will make searching and retrieving
this type of information very easy.  However at this time we can only
provide the raw data files for the sixteen Saccharyomyces cerevisiae
chromosomes used to generate the Riles-Olson physical map. These data
files are available via Internet Gopher, World Wide Web (ie. Mosaic),
and Anonymous FTP:

Use a Gopher client (like TurboGopher) to connect with
genome-gopher.stanford.edu, on Unix and VMS computers just use "gopher
genome-gopher.stanford.edu". With TurboGopher choose "Another
Gopher..." under the file menu and enter the host name
genome-gopher.stanford.edu

Using a WWW client (like Mosaic) enter the URL
"gopher://genome-gopher.stanford.edu" after choosing Open.

Move into the Saccharomyces Information folder:

      1.  About the Saccharomyces Genome Information Server
      2.  Help Searching the "<?>" database
      3.  Commonly Asked Questions about Gopher
      4.  ...
 -->  5.  Saccharomyces Information/
      6.  ...
      7.  FTP Archives for Molecular Biology/
      8.  Global Biological Information Servers by Topic/
      9.  Global Biological Information Servers/

Then move into the forth menu item:

      1.  Help Searching the "<?>" database
      2.  ...
      3.  Saccharomyces Genome version 0.0 <?>
 -->  4.  Olson Physical Map Restriction Fragment Data/
      5.  Saccharomyces Vector Sequences from GenBank/
      6.  ...
      7.  Sequenced Saccharomyces Genes -- LISTA release 3.1 <?>
      8.  Sequenced Saccharomyces Genes -- LISTA Homologies 3.1 <?>
      9.  Sequenced Saccharomyces Genes -- LISTA Documentation version 3.1
      10. ...
      11. ATCC Catalogs (courtesy of Johns Hopkins University)/
      12. E-mail Addresses of Yeast Reasearchers/
      13. Saccharomyces Genomic Information World Wide Web Server <HTML>
      14. Yeast BioSci Electronic Conference Archive Index <?>

For Anonymous FTP:

Connect to host name genome-ftp.stanford.edu as user anonymous and
enter your e-mail address as the password. Then
"cd pub/yeastdb/rest-frag-data" you will now be able to "get" any of the
data files you need. The "ls" or "dir" commands will display the names
of the available files.

Restriction fragment data is provided in sixteen files, one for each
chromosome. Each file contains seven columns of numbers separated by
tabs characters:

Column  Description
  1     Olson Clone Number
  2     Fragment Group Number
  3     Fragment Number
  4     Fragment Size in bp
  5     Standard Deviation of Size
  6     Left End Position in bp
  7     Right End Position in bp

(Fragments within a group are not ordered. However most groups only
contain one fragment.)

These files can be easily imported into Excel or other spreadsheets.
For Excel simply start the program then choose Open from the File menu
and pick the restriction fragment data file, for example XVI.frag.txt

The reference for six of these chromosomes:

Riles L; Dutchik JE; Baktha A; McCauley BK; Thayer EC; Leckie MP;
Braden VV; Depke JE; Olson MV. (1993) Physical maps of the six
smallest chromosomes of Saccharomyces cerevisiae at a resolution of
2.6 kilobase pairs. Genetics 134: 81-150

An example of a cosmid from chromosome VIII just to the right of put2
is:

6834    90      324     828     75      177674  178502
6834    90      325     761     60      178502  179263
6834    90      326     467     88      179263  179730
6834    91      327     1675    74      179730  181405
6834    92      328     2519    96      181405  183924
6834    93      329     5112    62      183924  189036
6834    94      330     649     46      189036  189685
6834    95      331     4244    54      189685  193929
6834    96      332     970     65      193929  194899
6834    96      333     793     76      194899  195692
6834    96      334     407     131     195692  196099

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

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