Hello, Yes, Rfam annotated the Celera rat assembly (available from NCBI as an alternate assembly). Unfortunately we don't have coordinate conversion data for that assembly.
Scroll to Genome Projects for a list of data releases: http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=10621 For the reference assembly, search "Genome Project" with the project ID "10629" For the alternate assembly, search "Genome Project" with the project ID "13999" http://www.ncbi.nlm.nih.gov/sites/entrez Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Zhi-Qiang Ye" <[email protected]> wrote: > From: "Zhi-Qiang Ye" <[email protected]> > To: "genome" <[email protected]> > Sent: Thursday, February 4, 2010 1:57:44 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Rfam annotations in UCSC genome browser? > > Dear Sir, > > It seems that there are not Rfam annotations for rat in UCSC > genome browser, > aren't there? So I read the website of Rfam, and find there are > coordinates for rat > RNAs. However, these coordinates are not based on rn4. > (http://rfam.sanger.ac.uk/genome/10116#tabview=tab1) > For example, chromosome 2 is 'CM000232', an entry that could be found > in NCBI > nucleotide database. It seems that this is a different assembly for > the rat genome. > If I don't want to use BLAT, can I convert their coordinates from > this > assembly to > rn4? > > Thanks! > > > Best regards, > Zhi-Qiang > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
