Hello,
I contacted UCSC in April of last you inquiring about a potential
update of the rat genome. Ann Zweig indicated that an update was
anticipated in early 2010. Is there a more firm deadline for this
update? I ask because we are about to invest a significant amount of
time and money into some custom rat arrays, and if the genome is going
to be updated this month or the next, we would hold off until better
sequence is available. Thanks again for your hard work,
James
Re: [Genome] Rat Genome > Nov. 2004
Ann Zweig
Wed, 22 Apr 2009 16:01:19 -0700
Hello James,
Unfortunately, due to some problems that were uncovered with the new
4.0 rat
assembly, Baylor has decided to not move forward with it. Instead, they will be
addressing the problems in a 4.x assembly which they estimate will be available
in early 2010.
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
James Srinivasan wrote:
> I was wondering when the new UCSC Rattus norvegicus genome build was going to
> come out? I looked over the previous lists of inquiries on this server, and
> have found several people asking the same question. They have all been
> directed to a page at Baylor that does not exist anymore
> (http://www.hgsc.bcm.tmc.edu/projects/rat/) which illustrates how long it has
> been since the genome has been updated.
>
> If you explore the Baylor site you find this page
> http://www.hgsc.bcm.tmc.edu/project-species-m-Rat.hgsc?pageLocation=Rat which
> seems to be the newer "rat genome project" page. However, while they mention
> an effort to update the rat genome, no expected date is listed. A white
> paper is listed, with a list of errors and issues with the Nov 2004 build of
> the rat genome such as the complete lack of the Y chromosome and the 5MB
> region of chromosome 1. Based upon the text, the white paper was written
> ~1.5 years after the 2004 v3.4 genome went up, and predicts it will take a
> year to finalize the new build.
>
> This paper http://www.nature.com/ng/journal/v40/n5/pdf/ng0508-523.pdf,
> written by people at UCSC, Baylor and other institutions indicates that the
> plan is for a "genome upgrade planned for early 2008."
>
> In the current funding environment, I understand that some things have to be
> changed or put on hold until more money is available. It is also acceptable
> if it was decided not to pursue an update of this genome. But it would be
> nice if either Baylor or UCSC could update the research community on the
> expected timeline since all previous deadlines are long past. Thank you for
> your time and efforts.
> James
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