Good Afternoon James: The latest news we have (18 Dec 2009) from the Rat Genome Project is that they are working on a version Rnor_4.1 but do not expect to have it finished until near the end of 2010.
--Hiram [email protected] wrote: > 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 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
