Hello, We do not include a RefSeq mitochondrial annotation track as part of the main browser, but the data set is small enough to perform a BLAT on our server to generate your own alignments. The idea would be to obtain the fasta sequences from NCBI, load them into the web BLAT tool, and run the program.
Please note that the defaults for the web BLAT tool are different than those we use when generating the RefSeq track (in particular, the option "-fine" is used for track creation). http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign http://genome.ucsc.edu/FAQ/FAQblat http://genomewiki.cse.ucsc.edu/index.php/Blat_Scripts If you want to run these on your own, download BLAT and set up a server and adjust the options as desired. The resulting PSL file can be loaded back as a custom track to view in the browser (refSeqAli is in PSL format). refFlat in in genePred format - which would require more additional processing to incorporate the CDS information refGene is also in genePred format - but with some extra details added in http://genome.ucsc.edu/FAQ/FAQformat Hopefully one of these options will work for your project, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Ziedulla Abdullaev (NIH/NIAID) [C]" <[email protected]> wrote: > From: "Ziedulla Abdullaev (NIH/NIAID) [C]" <[email protected]> > To: "[email protected]" <[email protected]> > Sent: Wednesday, January 20, 2010 9:04:09 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] annotation ofr human mitochondrial genome > > Hello > > I am interested in analysis of mitochondrial genome. I was looking at > refFlat.txt > <http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refFlat.txt.gz> > and > refGene.txt<http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz> > (hg18) and it looks like to me that they do not contain full > annotations for mitochondrial genes. I found only 3 annotations for > microRNAs in these files. When I checked GeneBank RefSeq for > mitochondrial genome (NC_012920 ) it contains 13 gens, 2 rRNAs, and 22 > tRNAs. Is there any way to generate refFlat- and refGene-files using > RefSeq? > > Thank you, > Ziedulla Abdullaev, Ph.D. > LIP, NIAID, NIH > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
