Hello, You are correct - the hg12 assembly is no longer supported by the tools BLAT, Convert, etc using the archive browser.
http://genome-archive.cse.ucsc.edu/goldenPath/28jun2002/liftOver/ has hg12-hg16 I will forward the request and see if a reverse of the file can be created (or published). Meanwhile, if you have the sequence data from hg16 and access to a server to run BLAT or another alignment program, the hg12 genome could be downloaded (or just the chrom/contig where you expect to find the match) and an alignment could be generated. This might be the best method anyway if you want to tune the parameters for the match to be found/optimized for a single gene, especially when using an older version of the draft genome. I will get back you once the liftOver question is addressed. If you don't hear back in a week or so, please send a reminder email, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "meritxell oliva pavia" <[email protected]> wrote: > From: "meritxell oliva pavia" <[email protected]> > To: [email protected] > Sent: Tuesday, December 15, 2009 8:52:00 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] hg12 coordinates > > Hi, > > I'm trying to get the coordinates of CDS exons, UTR exons 200 b > downstream and 200 b Upstream for hg12, but this human genome assembly > > seems not to be present in the menu of UCSC table browser. > If I have such genomic elements coordinates for hg16 and I want to use > > liftover tool for the conversion, I should use > *hg16ToHg12.over.chai*n > as a map.chain, right? > Where can I get this file? It's not present in hg12 archive, where u > can > only find hg12ToHg16.over.chain. > By the way, is there a better alternative to retrieve these data? > > Thanks a lot! > > -- > Meritxell Oliva > PhD Student > Comparative Bioinformatics Group > Bioinformatics and Genomics Programme > > Centre de Regulacio Genomica (CRG) > Dr. Aiguader, 88 > 08003 Barcelona > Spain > > email: [email protected] > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
