chromosome VI

Francis Ouellette francis at BORDUAS.NLM.NIH.GOV
Sun Feb 26 16:41:08 EST 1995


> From: macdiarm at sbsu1.auckland.ac.nz (Colin MacDiarmid)
> Subject: chromosome VI

> Recently I mapped a yeast clone to chromosome VI with OFAGE or a
> similar technique. I have sequence from this clone and it is not in the
> public databases.  I sent the sequence to MIPS and there was no hit in
> the private databases either.  Looking up chromosome VI sequencing
> plans I find the entire sequence should be in the private database.
> Why didnt I get a hit on this database?  Suggestions to the newsgroup
> or email me direct please.

Dear Colin,

the problem with private databases, is that they are private ;-)

MIPS holds the European (EC funded) private databases, and chromosome
VI was done, and is kept by the Japanese group.

(see last summary of Yeast Genome sequencing effort below)

The coordinator of chr VI is:

MURAKAMI, yasufumi              YASUFUMI at RTCS1.RIKEN.GO.JP

So you may want to check with him.  

The estimated release for chr VI is May, 1995

So the moral of the story, is that if it's not in one pprivate
database, it may be in an 'other', and there are many 'other'.


(I am just including the summaries, and the chr VI specific information)


best regards,

francis

--
| B.F. Francis Ouellette  
|
| francis at ncbi.nlm.nih.gov   

=========================================================================


> From mordant at fysa.ucl.ac.be Wed Feb 15 06:07 EST 1995

************************************************************************
*                                                                      *
*  PROGRESS REPORT FOR THE SYSTEMATIC SEQUENCING OF THE YEAST GENOME   *
*                                                                      *
************************************************************************

     **************************************************************
     *                                                            *
     *            GLOBAL STATUS ON JANUARY 31, 95                 *
     *                                                            *
     **************************************************************


1 - Country or Union funding genome sequencing effort 
2 - Principal investigator
3 - Sequenced length of chromosome or section in kb
4 - Estimation of the total length of chromosome or section in kb
5 - Sequenced length / Total length x 100 in %
6 - New sequences since last report (not necessarily public)
7 - Length of sequenced chromosome or section in kb which is 
    publically available (In EMBL/DDBJ/GenBank)
8 - Public length / Total length x 100 in %


------------------------------------------------------------------------
                  (1) (2)          (3)     (4)    (5)   (6)    (7)   (8)
                                  (kb)    (kb)    (%)  (kb)   (kb)   (%)
------------------------------------------------------------------------
				
CHR I            CAN  BUSSEY       223     223   100%     0    233  100%
CHR II           EU   FELDMANN     807     807   100%     0    807  100%
CHR III          EU   OLIVER       314     314   100%     0    314  100%
CHR IV RIGHT 1   USA  JOHNSTON       0     150     0%     0      0    0%
CHR IV RIGHT 2   USA  DAVIS          0     350     0%     0      0    0%
CHR IV LEFT 1    UK   BARRELL      180     540    33%   141    180  100%
CHR IV LEFT 2    EU   JACQ         231     600    38%     0     33   14%
CHR V            USA  DAVIS        569     569   100%     0    569  100%
CHR VI           JAP  MURAKAMI     270*    270   100%     0     20    7%
CHR VII          EU   TETTELIN     644    1150    56%    25     35    6%
CHR VIII         USA  JOHNSTON     563     563   100%     0    563  100%
CHR IX           UK   BARRELL      440     440   100%     0    440  100%
CHR X            EU   GALIBERT     727     735    99%     3    121   17%
CHR XI           EU   DUJON        666     666   100%     0    666  100%
CHR XII RIGHT    USA  JOHNSTON     403     750    54%   217    403  100%
CHR XII LEFT     EU   HOHEISEL      37     450     8%     0     37  100%
CHR XIII         UK   BARRELL      239     910    26%    48    239  100%
CHR XIV          EU   PHILIPPSEN   665     810    82%     0    116   18%
CHR XV           EU   DUJON        406    1150    35%    30     39   10%
CHR XVI RIGHT 1  UK   BARRELL        0     300     0%     0      0    0%
CHR XVI RIGHT 2  USA  JOHNSTON       0     150     0%     0      0    0%
CHR XVI LEFT 1   CAN  BUSSEY        10     300     3%     0     10  100%
CHR XVI LEFT 2   EU   GOFFEAU        0     300     0%     0      0    0%
				
------------------------------------------------------------------------
TOTAL YEAST GENOME                7396   12500  59,2%   465   4817   65%
------------------------------------------------------------------------


     K. Kleine                      P. Mordant and A. Goffeau
        MIPS          and         University of Louvain-La-Neuve
      Germany                              Belgium


 
 
    ***************************************************************
     *                                                            *
     *                   DETAILLED INFORMATIONS                   *
     *                                                            *
     **************************************************************


Coordinator :   Up today        Public      Confidential  Estimated length
                (kb)    %     (kb)     %     (kb)     %      (kb)     %

EU  (Goffeau)   4497  61%    2169    48%     2329   52%      6982   56%
USA (Johnston)   966  13%     966   100%        0    0%      1613   13%
UK  (Barrel)     859  12%     859   100%        0    0%      2190   17%
USA (Davis)      569   8%     569   100%        0    0%       919    7%
JAP (Murakami)   270   4%      20     7%      250   93%       270    2%
CAN (Bussey)     234   3%     234   100%        0    0%       523    4%
-----------------------------------------------------------------------
TOTAL           7396 100%    4817            2579           12500  100%


LISTA 4 : About 2 Mb of additional single genes sequences are available in
          EMBL + GENBANK see e.g. LISTA 3 (linder at urz.unibas.ch) for
          more informations.


MIPS : Requests for searches (DNA/protein) against the confidential dataset
       of YEAST sequences stored at MIPS can be sent to the following email
       address : becker at mips.embnet.org
       GCG-formated sequences and a short description of the intentions are
       preferable.

       These data are steadily released (see YEAST issues).


SGD : The Saccharomyces Genome Database of Standford (SGD or SacchDB) is
      available at the WWW server. To access this information using one
      of the many WWW clients simply "Open URL" and enter the following
      information : http://genome-www.stanford.edu/

      Contacts for the Saccharomyces Genome Database Project (SGD) :
      e-mail : yeast-curator at genome.stanford.edu
      ftp :    genome-ftp.stanford.edu
      Gopher : genome-gopher.stanford.edu
      WWW :    http://genome-www.stanford.edu/
      Tel :    415-723-8956
      Fax :    415-723-7016


---------------------------------------------------------------------------



---------------------------------------------------------------------------


(*) CHR VI (Public sequences) :  MURAKAMI (and BARRELL) 19 882 bp


Nr   Group       Locus      Accession     Size        Date
                              Number      (bp)

1    Barrell     SC6584       Z46255     19 882     24/10/94
                                        --------------------
                                         19 882 bp  31/01/95

NB : 270 000 bp by MURAKAMI are still terminated, still confidential and
     will be public in May 95.

---------------------------------------------------------------------------





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