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Sequence data discussed but not deposited

Francis Ouellette francis at monod.Biol.McGill.CA
Wed Mar 10 00:26:00 EST 1993

robison1 at husc10.harvard.edu (Keith Robison) writes:

>I would like the net readership's opinion of the following situation.
>I am not trying to start trouble, only to find out whether people
>believe the case in question to be a problem or not.

>The paper in question is:

>  MJ Mahan, JM Slauch, and JJ Mekalanos.
>  1993.  Science 259:686-688
>  Selection of bacterial virulence genes that are specifically induced
>  in host tissues.

[ description of interesting paper removed ]

>The paper states that 15 insertions and their flanking DNA were sequenced,
>and these broke down into five different genes.  Two of these genes 
>"showed no significant homology to sequence in GenBank".  4 paragraphs
>of the paper are devoted to describing the sequences found and interpreting
>their significance.

>Where are the sequences?  No accession number is listed in the paper.
>No actual sequence data is presented in the paper.  A search of
>NCBI's RETRIEVE server with the authors found nothing.    

>So, what do y'all think?

Dear Keith,

I think that you are not starting trouble, but are pointing to a
troubling problem, a varaint of which I have come accross too.  
It was another
journal and the authors actually had a boggus EMBL number in
their article.  This article came out last October, and their sequence
has still to show up.  I checked with update at ncbi.nlm.nih.gov and at 
update at EMBL-Heidelberg.DE, and the people at Heidelberg checked the
Japanese database for me.  The sequence accession number is wrong.  So
they (the authors of that article) by-passed the requirement by
providing a false number.  How to avoid this?  It seems simple enough
to me, the Journals should be allowed access to HUP (Hold Until 
Puplished) sequences, and should therefore check that the number is
indeed real.  This would assure that the no errors (real or
accidents!) would get introduced in the journal.

I have refrained from mentioning the article in question.  Their
sequence is in the paper, and as far as I am concerned, our copy of
the same gene is in the database, and therefore, this is the one that
people will find, and refer too ... we end up winning anyways, even if
our paper came out later :-)  (our sequence does refer to their paper
for conflicts, but this was after someone typed in (correctly!) the
gene in question ... which is something that we should not have to do
in this day and age!!)



| B.F. Francis "YES on YEAST" Ouellette  
| manager, yeast chromosome I & XVI sequencing project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis at monod.biol.mcgill.ca

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