Gopher access to LISTA version 3

Mike Cherry cherry at GENOME.STANFORD.EDU
Wed Sep 22 14:28:59 EST 1993


Access to the newly released LISTA, compilation of yeast nucleotide
sequences by Linder et al., is now available via the yeast genome
database genome. The yeast genome database gopher is available from
the computer named genome-gopher.stanford.edu.

The physical map views available via Gopher have also been updated.
(These views include clones that are available from the ATCC.) When an
association is know between a gene and a clone the gene name is
presented next to all occurances of the clone number.

When first connected to genome-genome.stanford.edu you should see the
menu:

      3.  Commonly Asked Questions about Gopher.
 -->  4.  Saccharomyces Genome version 0.0 <?>
      5.  Sequenced Saccharomyces Genes -- LISTA Documentation.
      6.  Sequenced Saccharomyces Genes -- LISTA release 3 <?>

The "Saccharomyces Genome" item includes LISTA3, the physical map
views and more.


Select item 4 and enter a gene symbol or clone number. For example
entering adh3 results in:


      1.  Gene Name  (LISTA) : ADH3.
      2.  Contig View of ATCC Clone number 70789.
      3.  Contig View of ATCC Clone number *9532*.
      4.  Contig View of ATCC Clone number 70050.
      5.  Contig View of ATCC Clone number 71105.
      6.  Contig View of ATCC Clone number 71028.
      7.  Contig View of ATCC Clone number 71069.
      8.  Contig View of ATCC Clone number 71044.
      9.  Contig View of ATCC Clone number 70442.
      10. Contig View of ATCC Clone number 70819.
 -->  11. Contig View of ATCC Clone number 70708.
      12. Contig View of ATCC Clone number 70456.
      13. Contig View of ATCC Clone number 70734.
      14. Contig View of ATCC Clone number 70046.
      15. Contig View of ATCC Clone number 70697.
      16. Contig View of ATCC Clone number 70261.
      17. Contig View of ATCC Clone number 70652.
      18. Contig View of ATCC Clone number 70651.
      19. Contig View of ATCC Clone number 70186.
      20. Contig View of ATCC Clone number 70976.
      21. Contig View of ATCC Clone number 70671.
      22. Gene Symbol: adh3.


Selecting item 1 retreives the LISTA release 3.0 information on ADH3:

Gene Name  (LISTA) : ADH3
EMBL information   : EMBL; K03292; SCADH3.
Length of Sequence : 1125
Codon Bias         : 0.402
Reference          : UNPUBLISHED.


Selecting item 11 retrieves a view of a small portion of the physical
map:


Contig View of ATCC Clone number 70708
Washington Univ Clone number 6364
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== adh3
                                  --70456--
                                    ---70734---
                                        --70046-- ypk2
                                          --70697-- ilv2
                                             --70261--
                                                 --70652--
                                                     --70651--
                                                        --70186-- sto1
                                                          -----70976-----
Note: Asterick (*) marks prime clones not available from ATCC.

See the item called 'Help Searching the "<?>" database' on the first
menu for suggestions on formulating queries.

This Gopher server is still very much in development and your comments
and suggestions are requested.


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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