31/03/95 : PROGRESS REPORT OF THE YEAST GENOME SYSTEMATIC SEQUENCING

Francis Ouellette francis at BORDUAS.NLM.NIH.GOV
Wed Apr 26 14:45:21 EST 1995


just passing it along ...  

Thank you to Philippe Mordant, Andre Goffeau and Karl Kleine For
putting this together, and to all the YEAST genome sequencing labs for
making their sequences available for all of us to use.

regards,

francis

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



----- Begin Included Message -----

> From: mordant at fysa.ucl.ac.be (Philippe Mordant)
> Subject: 31/03/95 : PROGRESS REPORT OF THE YEAST GENOME SYSTEMATIC SEQUENCING

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

     **************************************************************
     *                                                            *
     *            GLOBAL STATUS ON MARCH 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      276     540    51%    58    276  100%
CHR IV LEFT 2    EU   JACQ         282     600    47%    14     74   28%
CHR V            USA  DAVIS        569     569   100%     0    569  100%
CHR VI           JAP  MURAKAMI     270*    270   100%     0     20    7%
CHR VII          EU   TETTELIN     736    1150    64%    36     82   11%
CHR VIII         USA  JOHNSTON     563     563   100%     0    563  100%
CHR IX           UK   BARRELL      440     440   100%     0    440  100%
CHR X            EU   GALIBERT     726     735    99%     0    129   18%
CHR XI           EU   DUJON        666     666   100%     0    666  100%
CHR XII RIGHT    USA  JOHNSTON     542     750    72%     0    542  100%
CHR XII LEFT     EU   HOHEISEL      74     450    16%     0     37   50%
CHR XIII         UK   BARRELL      377     910    41%   104    377  100%
CHR XIV          EU   PHILIPPSEN   713     810    88%    34    116   16%
CHR XV           EU   DUJON        513    1150    45%    90     83   16%
CHR XVI RIGHT 1  UK   BARRELL       26     300     9%     0     26  100%
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                8126   12500  65,0%   335   5355   66%
------------------------------------------------------------------------


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


 
 
     **************************************************************
     *                                                            *
     *                    DETAILED INFORMATION                    *
     *                                                            *
     **************************************************************


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

EU  (Goffeau)   4830  59%    2309    48%     2521   52%      6982   56%
UK  (Barrel)    1118  14%    1118   100%        0    0%      2190   17%
USA (Johnston)  1105  14%    1105   100%        0    0%      1613   13%
USA (Davis)      569   7%     569   100%        0    0%       919    7%
JAP (Murakami)   270   3%      20     7%      250   93%       270    2%
CAN (Bussey)     234   3%     234   100%        0    0%       523    4%
-----------------------------------------------------------------------
TOTAL           8126 100%    5355            2771           12500  100%


LISTA 3 : 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 database SacchDB distributed by the Saccharomyces Genome Database
      project of Stanford (SGD) is available at the Stanford 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 I (Public sequences) :  BUSSEY  223 123 bp


The complete sequence can be retrieved by FTP to the following addresses :

ftp.ebi.ac.uk (193.62.196.6)          soon   (/pub/databases/yeast/chrI)
ftp.mips.embnet.org (141.61.66.2)     soon      ([anonymous.yeast.chrI])
genome-ftp.stanford.edu (36.69.0.79)        (/pub/yeast/genome_seq/chrI)
ncbi.nlm.nih.gov (130.14.25.1)        soon      (/repository/yeast/chrI)


 
Nr   Cosmid   Accession   Size      Date
              Number      (bp)

1   SCU12980   L12980   103 411     19/01/95
2   YSCLTE1A   L20125     6 344     13/10/94 (reversed compared to contig!)
3   YSCLTESPO  L05146    29 410     13/10/94
4   YSCCHROMI  L22015    41 987     18/04/94
5   YSCCHR1RAA L28920    53 975     13/02/94
    overlaps             -8 227    
                        ---------------------
                        226 900 bp  01/03/95


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


CHR II (Public sequences) :  FELDMANN  807 188 bp


The complete sequence can be retrieved by FTP to the following addresses :

ftp.ebi.ac.uk (193.62.196.6)                  (/pub/databases/yeast/chrII)
ftp.mips.embnet.org (141.61.66.2)                ([anonymous.yeast.chrII])
genome-ftp.stanford.edu (36.69.0.79)         (/pub/yeast/genome_seq/chrII)
ncbi.nlm.nih.gov (130.14.25.1)                   (/repository/yeast/chrII)


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


 
CHR III (Public sequences) :  OLIVER  315 338 bp


The complete sequence can be retrieved by FTP to the following addresses :

ftp.ebi.ac.uk (193.62.196.6)                 (/pub/databases/yeast/chrIII)
ftp.mips.embnet.org (141.61.66.2)               ([anonymous.yeast.chrIII])
genome-ftp.stanford.edu (36.69.0.79)        (/pub/yeast/genome_seq/chrIII)
ncbi.nlm.nih.gov (130.14.25.1)                  (/repository/yeast/chrIII)


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


CHR IV RIGHT 1 (Public sequences) :  JOHNSTON      0 bp



Nr   Cosmid      Locus      Accession    Size        Date
                              Number     (bp)

-      -           -             -         -           -
                                       --------------------
                                             0 bp  31/03/95


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


CHR IV RIGHT 2 (Public sequences) :  DAVIS      0 bp



Nr   Cosmid      Locus      Accession    Size        Date
                              Number     (bp)

-      -           -             -         -           -
                                       --------------------
                                             0 bp  31/03/95


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


CHR IV LEFT 1 (Public sequences) :  BARRELL  275 773 bp


Nr   Cosmid      Locus      Accession    Size        Date
                              Number     (bp)

1     9395       SC9395       Z46727    39 335     20/11/92
2     8554       SC8554       Z46796    38 760     25/11/94
3     8557       SC8557       Z47746    36 217     17/01/95
4     9813       SC9813       Z47814    14 825     26/01/95
5     9489       SC9489       Z47813    13 631     26/01/95
6     8119       SC8119       Z48008    37 404     28/01/95
7     9302       SC9302X      Z48179    37 552     07/02/95
8     9346       SC9346       Z48784    19 236     25/03/95
9     9727       SC9727       Z48758    38 813     23/03/95
                                       --------------------
                                       275 773 bp  31/03/95


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


 
CHR IV LEFT 2 (Public sequences) :  JACQ  74 193 bp


Nr   Group       Locus      Accession    Size        Date
                              Number     (bp)

1   Foury       SCCHROIV     X82086     32 821     14/10/94
2   Urrestarazu SCCHRIV42    Z48432     41 372     21/02/95
                                       --------------------
                                        74 193 bp  31/03/95


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


CHR V (Public sequences) :  DAVIS  569 202 bp


The complete sequence can be retrieved by FTP to the following addresses :

ftp.ebi.ac.uk (193.62.196.6)          soon   (/pub/databases/yeast/chrV)
ftp.mips.embnet.org (141.61.66.2)     soon      ([anonymous.yeast.chrV])
genome-ftp.stanford.edu (36.69.0.79)        (/pub/yeast/genome_seq/chrV)
ncbi.nlm.nih.gov (130.14.25.1)        soon      (/repository/yeast/chrV)


Assembly of chromosome V from cosmids submissions to Genbank :

Nr  Locus   Accession   Size     Date      from     to    overlap to
              Number    (bp)                             previous cosmid

1  SCE9669    U18795   50 849   21/12/94      1    50 849        0
2  SCE8199    U18779   36 872   19/12/94    301    36 872      300
3  SCE9871    U18530   62 643   19/12/94    305    62 643      304
4  SCE9537    U18778   66 030   19/12/94    329    66 030      328
5  SCE9379    U18796   43 100   21/12/94    181    43 100      180
6  SCE6592    U18813   40 565   21/12/94    202    40 565      201
7  SCE3612    U18814    8 443   21/12/94    161     8 443      160
8  SCE9747    U18839   64 797   21/12/94   1505    64 797    1 504
9  SCE9781    U18916   68 303   21/12/94    701    68 303      700
10 SCE8229    U18917   67 883   21/12/94    401    67 883      400
11 SCE9163    U18922   64 044   21/12/94    251    64 044      250
                                                  ----------------
                                                  573 529  - 4 327
                                                  ----------------
                                                      569 202 bp


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


(*) 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  31/03/95

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

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


 
CHR VII (Public sequences) :  TETTELIN   81 678 bp


Nr   Group       Locus      Accession     Size        Date
                              Number      (bp)

1    Foury       S58126       S58126     16 956     10/07/90
2    Foury     SCDNAORFS      X83099     18 258     16/12/94
3    Bruschi   SCDNACVII      X84705     11 100     17/02/95
4    Oliver    SCCHVII35      Z48618     35 364     07/03/95
                                        --------------------
                                         81 678 bp  31/03/95


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


CHR VIII (Public sequences) :  JOHNSTON  562 638 bp


The complete sequence can be retrieved by FTP to the following addresses :

ftp.ebi.ac.uk (193.62.196.6)                (/pub/databases/yeast/chrVIII)
ftp.mips.embnet.org (141.61.66.2)              ([anonymous.yeast.chrVIII])
genome-ftp.stanford.edu (36.69.0.79)       (/pub/yeast/genome_seq/chrVIII)
ncbi.nlm.nih.gov (130.14.25.1)                 (/repository/yeast/chrVIII)

Nr   Cosmid   Accession   Size      Date
              Number      (bp)

1   YSCH9196   U11583     55 070     05/07/94
2   YSCH9433   U11582     29 276     05/07/94
3   YSCHL5018  U11581     16 274     10/07/94
4   YSCH9780   U10555     24 431     21/06/94
5   YSCHL2825  U10400     18 715     21/06/94
6   YSCH8082   U10399     28 124     21/06/94
7   YSCH8179   U00062     44 113     19/05/94
8   YSCH8025   U00061     27 816     18/05/94
9   YSCH9205   U10556     39 203     21/06/94
10  YSCH9332   U00060     36 176     18/05/94
11  YSCH8263   U00059     39 954     11/05/94
12  YSCH9315   U10398     30 350     21/06/94
13  YSCH9666   U10397     39 057     21/06/94
14  YSCH9986   U00027     41 663     26/02/94
15  YSCH9186   U00028     10 801     26/02/94
16  YSCH9998   U00030     35 600     26/02/94
17  YSCH9177   U00029     52 664     26/02/94
    overlaps              -6 652     01/09/94
                         --------------------
                         562 638 bp  31/09/94


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


CHR IX (Public sequences) :  BARRELL  439 885 bp

The complete sequence of chr IX has been submitted in one piece :

Nr   Cosmid   Accession   Size      Date
              Number      (bp)

1    chr IX    Z47047    439 885     22/12/94
                         --------------------
                         439 885 bp  22/12/94

 
The list of the 14 separate cosmids :

Nr   Cosmid   Accession   Size      Date
              Number      (bp)

1     9877     Z37996     17 731     06/10/94
2     9167     Z37997     17 421     06/10/94
3    L4357     Z38062     75 317     12/10/94
4    L5610     Z38060     37 730     12/10/94
5     9168     Z38113     42 793     12/10/94
6     9687     Z38059     21 431     12/10/94
7     4554     Z38061     19 817     15/10/94
8     9150     Z38125     43 504     18/10/94
9     9910     Z46728     25 761     20/11/94
10    8277     Z46833     26 142     30/11/94
11    9905     Z46861     33 954     02/12/94
12    3299     Z46881     30 977     05/12/94
13    8224     Z46902      8 956     07/12/94
14    9402     Z46921     38 990     09/12/94
        overlaps            -639     22/12/94
                         --------------------
                         439 885 bp  22/12/94


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


CHR X (Public sequences) :  GALIBERT  128 853 bp


Nr   Group       Locus      Accession     Size        Date
                              Number      (bp)

1   Zimmermann  SJ100567      X77087     9 464     02/08/94
2   Galibert    YSCSEQA       L26347     8 236     07/08/94
3   Hilger      SCXLTEL       Z34098    40 257     03/06/94
4   Hilger      SCXCDNA       Z34288    17 137     09/06/94
5   Foury       SCPRP21       X77688    36 016     22/09/94
6   Zimmermann  SCXBCK1       X77923     9 743     24/01/95
7   Hilger      SCCHRXLTE     Z48148     8 000     03/02/95    
                                       --------------------
                                       128 853 bp  31/03/95


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


CHR XI (Public sequences) :  DUJON  666 448 bp


The complete sequence can be retrieved by FTP to the following addresses :

ftp.ebi.ac.uk (193.62.196.6)                  (/pub/databases/yeast/chrXI)
ftp.mips.embnet.org (141.61.66.2)                ([anonymous.yeast.chrXI])
genome-ftp.stanford.edu (36.69.0.79)         (/pub/yeast/genome_seq/chrXI)
ncbi.nlm.nih.gov (130.14.25.1)                   (/repository/yeast/chrXI)


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


 
CHR XII RIGHT (Public sequences) :  JOHNSTON  542 172 bp


Nr   Cosmid      Locus      Accession     Size        Date
                              Number      (bp)

1     8167     YSCH8167       U14913     38 868     23/09/94
2     8479     YSCL8479       U17244     32 494     23/11/94
3     9328     YSCL9328       U17245     14 827     23/11/94
4     9470     YSCL9470       U17246     40 738     23/11/94
5    L2142     YSCLL2142      U17247     19 198     23/11/94
6     8003     YSCL8003       U17243     40 214     07/12/94
7     8083     YSCL8083       U19027     41 454     15/01/95
8     8300     YSCL8300       U19028     37 541     15/01/95
9     9638     YSCL9638       U19102     15 175     15/01/95
10    8039     YSCL8039       U19103     31 806     15/01/95
11   L3502     YSCLL3502      U19104     22 761     15/01/95
12    8084     YSCL8084       U19729     40 197     30/01/95
13    9931     YSCL9931       U20162     28 149     30/01/95
14    8543     YSCL8543       U20618     37 729     10/02/95
15    9672     YSCL9672       U20865     40 455     11/02/95
16    9576     YSCL9576       U20939     35 805     14/02/95
                                        --------------------
                                        542 172 bp  31/03/95


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


CHR XII LEFT (Public sequences) :  HOHEISEL    37 396 bp



Nr   Group       Locus      Accession    Size        Date
                              Number     (bp)

1   Wambutt    SCCH13LST      Z47973    37 396     26/01/95
                                       --------------------
                                        37 396 bp  31/03/95

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


CHR XIII (Public sequences) :  BARRELL  377 162 bp


Nr   Cosmid      Locus      Accession    Size        Date
                              Number     (bp)

1     9514      SC9514        X80836    13 841     09/08/94
2     8175      SC8175        X80835    15 581     09/08/94
3     9745      SC9745        Z38114    19 975     15/10/94
4     8248      SC8248        Z46373    25 135     27/10/94
5     8337      SC8337        Z46659    34 506     15/11/94
6     9725      SC9725        Z46660    32 148     15/11/94
7     9958      SC9958        Z46729    20 951     20/11/94
8     9375      SC9375        Z47071    28 992     29/12/94
9     9827      SC9827        Z47816    20 668     26/01/95
10    9646      SC9646        Z47815    27 466     26/01/95
11    8054      SC8054        Z48430     9 421     21/02/95
12    9532      SC9532X       Z48502    24 105     28/02/95
13    8270      SC8270        Z48613    32 481     07/03/95
14    9553      SC9553        Z48622    16 279     08/03/95
15    9920      SC9920        Z48639    23 498     12/03/95
16    9408      SC9408        Z48756    15 848     22/03/95
                                       --------------------
                                       377 162 bp  31/03/95


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


 
CHR XIV (Public sequences) :  PHILIPPSEN   116 222 bp


Nr   Group       Locus      Accession    Size        Date
                              Number     (bp)

1   Volckaert   SCN200XG      X77395    23 901     01/06/94
2   Volckaert   SCXIV         X77114     8 887     02/08/94
3   Foury       SCN201952     X78898    35 161     24/11/94
4   Foury       SCDNAO        X83226     8 223     15/12/94
5   Gaillardin  SCRPD3COS     Z46259    40 050     18/01/95
                                       --------------------
                                       116 222 bp  31/03/95


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


CHR XV (Public sequences) :  DUJON  83 326 bp


Nr   Group       Locus      Accession    Size        Date
                              Number     (bp)

1   Schweizer   SCDNAIRA2     X75449    10 270     01/11/94
2   Schweizer   SCCHXVORF     X83121    39 307     07/12/94
    overlap with 1                     -10 270     07/12/94
3   Hilger      SCCHRXV44     Z48149    44 019     03/02/95
                                       --------------------
                                        83 326 bp  31/03/95


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


CHR XVI RIGHT 1 (Public sequences) :  BARRELL  25 540 bp



Nr   Cosmid      Locus      Accession    Size        Date
                              Number     (bp)

1     8132      SC8132X       Z48483    25 540 bp  24/02/95
                                       --------------------
                                        25 540 bp  31/03/95

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


CHR XVI RIGHT 2 (Public sequences) :  JOHNSTON      0 bp


Nr   Cosmid      Locus      Accession    Size        Date
                              Number     (bp)

-      -           -             -         -           -
                                       --------------------
                                             0 bp  31/03/95


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


CHR XVI LEFT 1 (Public sequences) :  BUSSEY  10 450 bp


Nr   Cosmid      Locus      Accession    Size        Date
                              Number     (bp)

1    Bussey     YSCKRE6A      L33835    10 450     21/06/94
                                       --------------------
                                        10 450 bp  31/03/95


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


CHR XVI LEFT 2 (Public sequences) :  GOFFEAU      0 bp



Nr   Group       Locus      Accession    Size        Date
                              Number     (bp)

-      -           -             -         -           -
                                       --------------------
                                             0 bp  31/03/95

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


----- End Included Message -----




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