Chr. 8 sequence is available

Mark Johnston mj at SEQUENCER.WUSTL.EDU
Fri Sep 30 13:26:24 EST 1994


Dear buddies,

        We have determined the DNA sequence of S. cerevisiae chromosome VIII.
 It was submitted to GenBank over the last several months (March-June) in
sub-chromosomal pieces. The complete, assembled sequence and feature tables
of chromosome VIII are now publicly available by anonymous ftp from:

        genome-ftp.stanford.edu [IP address 36.69.0.79] 

                in the /pub/yeast/genome_seq/chrVIII directory; 

        ncbi.nlm.nih.gov [IP address 130.14.25.1] 

                in the /repository/yeast/chrVIII directory; 

        mips.embnet.org [IP address 141.61.66.2] 

                in the [anonymous.yeast.chrVIII] directory. 

In addition, all of the individual GenBank entries can be retrieved using the 
accession numbers listed below from the NCBI retrieve server. Send a
message with 'help' (without the '') to retrieve at ncbi.nlm.nih.gov to learn
how to use this server.

Below is the README file that describes the information available by ftp.

        (Thanks go to Francis Ouellete and Petr Jordan for help with
 transferring and formatting the files; and to Francis Ouellete, Mike Cherry,
 and Werner Mewes for providing the ftp servers).

______________________________________________________

DESCRIPTION OF DATASET FOR Saccharomyces cerevisiae CHROMOSOME VIII

        The complete DNA sequence of yeast chromosome VIII was 
determined as described in the reference listed below.  The sequence was 
annotated and submitted to GenBank in 17 individual entries (names and 
accession numbers listed below).  Here we provide the complete assembled 
sequence (562,638 base-pairs), tables describing the features of the sequence,
 and a sequence database (in AScDB [R. Durbin and J-T. Mieg,  unpublished] 
for Sun Workstations (see below).  

REFERENCE 

Science, in press, (Sept. 30, 1994 issue):

Complete nucleotide sequence of S. cerevisiae  chromosome VIII

Johnston, M., Andrews, S., Brinkman, R., Cooper, J., Ding, H., Dover, J., 
Du, Z., Favello, A., Fulton, L., Gattung, S., Geisel, C., Kirsten, J.,
Kucaba, T., Hillier, L., Jier, M., Johnston, L., Langston, Y., Latreille,
P., Louis, E.J.,*Macri, C., Mardis, E., Menezes, S., Mouser, L., Nhan, M., 
Rifkin, L., Riles, L., St.Peter, H., Trevaskis, E., Vaughan, K., Vignati, D., 
Wilcox, L., Wohldman, P. Waterston, R. Wilson, R., and Vaudin, M.

                                Genome Sequencing Center
                                               and
                                    Department of Genetics

                         Washington University School of Medicine
                                            St. Louis, MO

*Yeast Genetics
  Institute of Molecular Medicine
  John Radcliffe Hospital
  Oxford OX3 9DU
  England


GENBANK ENTRY NAMES AND ACCESSION NUMBERS:

Cosmid entries are listed from left to right as they appear on the
 chromosome.  The cosmid entry names are also listed in the files 
chr8.ascii.table and chr8.word.table, with the genes and chromosome 
elements included in that entry listed below each entry name.

LOCUS           Accession
NAME            Number

YSCH9196                U11583
YSCH9433                U11582
YSCHL5018              U11581
YSCH9780                U10555
YSCHL2825              U10400
YSCH8082                U10399
YSCH8179                U00062
YSCH8025                U00061
YSCH9205                U10556
YSCH9332                U00060
YSCH8263                U00059
YSCH9315                U10398
YSCH9666                U10397
YSCH9986                U00027
YSCH9186                U00028
YSCH9998                U00030
YSCH9177                U00029


DESCRIPTION OF FILES INCLUDED ON THE FTP SERVERS:

chr8.fasta:               The complete sequence of chromosome VIII in fasta
                                  format.

chr8.table.ascii:      Table (in ASCII format) listing all major chromosomal
                                  elements and their starting position in
                                  order from the left end of the chromosome. 
                                  Includes a legend describing the table.

chr8.table.word:    Table (in Microsoft Word 5.1 for Mac format) listing all 
                                 major chromosomal elements and their
                                 starting position in order from the left
                                  end of the chromosome.  Includes a legend
                                  describing the table.

chr8.fea                 Table (in ASCII format) listing beginning and ending 
                                positions for ORFs, tRNAs, introns,
                                inverted repeats, direct repeats, each
                                GenBank submission,  and Ty  elements.

chr8.pep                File (fasta format) of predicted protein sequences
                                for all ORFs.

chr8.gb                   The complete sequence of chromosome VIII in GenBank 
                                format.  This record does not presently exist in
                                GenBank as one record (but only as the above 17 
                                records).

chr8.asn1               The complete sequence of chromosome VIII in ASN.1 
                                format.  This record does not presently exist in
                                GenBank as one record (but only as the above 17 
                                records).


chr8.proteins.tar.Z:    File (tar format) containing all predicted protein
                                       sequences in individual files.


chr8.ascdb.tar.Z:    AScDB database.  AScDB executable file for use on a Sun 
                                  Workstation running Solaris 2.3 is included. 

                        First type:
                                setenv ACEDB your_path_name/chr8db
                        then type:
                                your_path_name/chr8db/bin/xace
                        (further instructions for acedb are available
                        via anonymous ftp from ncbi.nlm.nih.gov in
                        the directory /repository/acedb)



CURATION:

Please notify Mark Johnston (mj at sequencer.wustl.edu) of any sequence errors.

The Saccharomyces Genome Database (SGD) project (developed by Mike
 Cherry and David Botstein,  Stanford University) will serve as curator for the 
sequence features.  Please notify them of any information you acquire about 
the chromsome VIII sequence and genes by sending a message to:

                                yeast-curator at genome.stanford.edu   

I hope all of you find the sequence useful!

Sincerely,


        Mark Johnston
        Department of Genetics Box 8232
        Washington University Medical School
        4566 Scott Ave.
        St. Louis, MO  63110
        FAX:   314-362-2985
        TEL:    314-362-2735
        E-mail:  mj at sequencer.wustl.edu  
            




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