Sequencing Report

francis at NCBI.NLM.NIH.GOV francis at NCBI.NLM.NIH.GOV
Sat Aug 26 14:41:06 EST 1995


> Steve Kron <kron at WI.MIT.EDU> wrote:

sk> Truly wonderful, the nearing completion of the sequencing will end the era
sk> of non-science that still persists--the proliferation of papers reporting a
sk> yeast gene that looks like a mammalian protein and little else.  Bravo
sk> again.  Soon we will all turn back to biology: pathways and biochemistry
sk> and physiology.  The effects on the literature are already obvious. 

> From: dan at cubsps.bio.columbia.edu (Dan Zabetakis)

dz>   Yes, but it won't be "we ... all". The yeast field will shrink very fast,
dz> and probably already is, as a proportion of total trained workers.
dz>   Once the genome is finished the main way that a young investigator got a
dz> grant and got published, and later got tenure, was thorugh the cloning of
dz> novel genes. No more will that be enough.


I would first like to say that I'm quite happy at the ammount of
discussion Phillipe Mordant's post has made.  I agree Steve that the
work done by the YEAST genome sequencing community is quite exciting,
and will lead to a different way we do and think about biology of
Saccharomyces.

I think some of the labs which the sequencing of yeast will continue
with their new found expertise, and will move on to sequence the DNA of
other organism (eg Bart Barrell is now doing some work on S. pombe
chromosome I), others will move to the 'natural' next phase of this
project which is to do the functional analysis of all these genes (eg
the EUROFAN project).  There will be yet another group who will be
happy to go back to the pre 1989 frenzy, and go back to the way things
where ... no examples cited here  ;-)

For the rest of the community there will now be a new tool they can use
for their work, and I also think the days are passed where you sequence
a gene, and you get a grant or a degree.   Poeple will continue to
screen for their favorite phenotype, and continue to do genetic and
biochemical/molecular analysis on these products, and it's just a short
piece of the experiment which will be faster, the sequencing and
figuring out of what the gene may be doing, and how that fits with the
phenotype you just discovered.  I predict we will find many surprises
there!

A point which may be obvious to the readers of this newsgroup, but
maybe not to the yeast community at large, is that the access to what
is know (via SGD WWW page at Stanford or Entrez at NCBI) will become an
_essential_ tool for yeast biologist ... and I hope scientist worldwide
will use these tools, and can therefore be on top of what is known for
a given gene, or gene familly.  The use of these tools will also be an
important 'modifier' of how these tools will evolve.  For example,
Entrez is introducing a genomes division which we will be demonstrating
at Hilton Head (Genome meeting in South Carolina in Sept. 95).  With
this new division we will be offering a new view on large records in
GenBank (yeast chrromosomes, complete mitochondrial genomes, H.
influenzae genomes etc).  The impetus for these changes does come from
the community, what they need, and how they want to work with the
data.  This is indeed a very exciting period to be needing genome
information to do your research.


Steve also wrote:

sk> However, one question: what is "confidential" data doing staying
sk> confidential?  I am a big fan of immediate release.  Is there still any
sk> argument for not releasing each cosmid size chunk as it is completed?  
sk> When can we expect for this policy to end?

and Mike Moser (moser at U.WASHINGTON.EDU) wrote:

mm>        I also want to put my vote in for full and immediate release of
mm> sequence as soon as it becomes available.  Of course no-one expects
mm> release of sequences that the researchers are not reasonably confident of,
mm> but if CHR X is 100% complete, then why not release it a soon as possible.

And here I want to specially thank the European coomunity yeast genome
sequencing groups for showing us these numbers and subjecting
themselves to some of the 'abuse' they are (undeservingly) getting.

Although chr X may be completly finished, I know that the EU (European
Union) group has a different way if 'finalizing' their sequence, and
that there is a QA (quality Assurance) phase a portion of the
sequencende is done again by other groups.  There is also a period
where you look back at your finished sequence, and you need to evaluate
if it is indeed "finished".  And I strongly believe that the EU has the
right and privaledge to write up their chr X paper and wait for it to
be accepted or published before they release the sequences, as are the
contract labs who did the individual cosmids.  They can submit their
sequence to GenBank/EMBL/DDBJ as they wish, when they publish (if they
do) their own cosmids, but these are not the 'EU' final proiduct.

This is a different philosophical approach than that of Barrell's
(Sanger Center) group, Bussey's  (McGill), Johnson's (Wash U) or Davis'
(Stanford)  but it cannot be dissmissed as the wrong way to do it, as
they have proven (quite clearly with the other chromosomes they
sequenced) that it works.

Mike also said:

mm> It gives the appearance that people are withholding the info for 
mm> their own benefit.  

and so they should ... they did the work, no?

mm> The people that have certainly deserve a
mm> great thank you from the entire world research community ...

yes, I'll second that, and a good place to stop here!

regards to all,

francis

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




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