How much yeast is known? [Re: Progress Report YEAST Genome Sequencing]

Mike Cherry cherry at fafner.Stanford.EDU
Sat Nov 12 12:34:20 EST 1994


In article <1994Nov12.071107.19651 at comp.bioz.unibas.ch>,
Reinhard Doelz <doelz at comp.bioz.unibas.ch> wrote:
>Mordant Philippe (pmordant at rc1.vub.ac.be) wrote:
>
>: *      IN EMBL + GENBANK + MIPS + SDB ON NOVEMBER 01, 1994          *
>: * PROGRESS REPORT FOR THE SYSTEMATIC SEQUENCING OF THE YEAST GENOME *
>
>Does this include MIPS sequences which are kept confidential, i.e. 
>not being available to the non-MIPS-customer research community? 

I believe the answer is yes. The numbers posted by Dr. Philippe appear
to include non-public sequences held at MIPS or at one of the other
sequencing centers around the world. These would be regions that are
considered almost done and now being annotated and verified, but not
yet submitted to the public databases.

Note that SGD, which might be what is referred to as SDB above, only
contains publicly available sequences.  That is, SGD does not contain
any sequences that are not already in GenBank/EMBL.

>:                           submitted     estimated	new in
>:                            up today     length		october 94
>:                                (kb)     (kb)	(%)	(kb)
>: TOTAL YEAST GENOME             5687   12400    46%    669
>
>As there is a considerable amount of yeast sequences already published 
>in the sequence database (with functions etc. assigned), what would be 
>a more customer-oriented guess on what fraction of sequences is available 
>to the community in the EMBL database? 

We estimate that 52% of the S. cerevisiae genome is present in
GenBank/EMBL.  This estimate includes some analysis that we have done
on yeast sequences in GenBank. We built a non-redundant set of
sequences, or a consensus sequence contig, out of the GenBank
sequences. When the consensus sequences are combined with the genomic
sequencing results we obtain a number of 6.4Mbp. The amount of
publicly available sequences expected from the genomic sequencing
projects should increase by 4Mbp in 1995. Thus it is advised that you
regularly search the GenBank/EMBL on the chance that your region of
interest has been made public.

Mike

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



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