Hello, You are correct, there is no UniGene track for mouse. The recommended track for genes is the UCSC Genes track (it combines several input sources and provides a comprehensive gene summary). However, you can create a Unigene custom track yourself by using BLAT.
The general idea is to install BLAT, obtain the query sequences from UniGene and the genomic sequence from UCSC, then run/filter the output (perhaps using rules similar to ours, as explained in the human UniGene track description page, Methods section). http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=uniGene_3 http://genome.ucsc.edu/FAQ/FAQblat http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Download Once completed, you can use the utility "pslToBed" from the Kent source tree to create the final BED file. http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities http://genome.ucsc.edu/FAQ/FAQdownloads#download27 You can load the data as a custom track in PSL or BED format to view your data versus other annotation if you wish. Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Pete Shepard" <[email protected]> wrote: > From: "Pete Shepard" <[email protected]> > To: [email protected] > Sent: Wednesday, December 2, 2009 9:39:11 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] unigene ids? > > Dear Browser, > > I am trying to convert unigene ids for mouse, eg "mm.1" , into > chromome > locations "bed format". Is there a way to accomplish this using the > browser? > > Also, I am curious as to why there is no unigene track for mouse? Is > there > an equivalent track that the browser uses? I know that there is a > knownIsoform track that clusters genes together, but this track only > contains ~26,000 clusters and unigene contains ~3x this amount? > > Thanks, > > Pete > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
