Hi Shannon, >>The end reads are available for each BAC, is the "between" sequence available?
You might try making a custom track with each item spanning the entire BAC. Then with the Table Browser, output as BED, then truncate to just the first 4 or 6 fields. Info on creating custom tracks can be found here: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks >> However, I'm not sure how to identify specific coordinates for the breakpoint in synteny. The Human Chain/net track is our best guess. You might also try liftOver (http://genome.ucsc.edu/cgi-bin/hgLiftOver) with the "Allow multiple output regions" option checked with your BAC span custom track. I hope that helps. Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 6/6/11 4:13 PM, Shannon Eileen Duke Becker wrote: > I have identified several regions of the dog genome (the regions are bounded > each by 2 BACs) I'm interested in translating to the human genome. I've used > the convert function using the end read coordinates for the BACs proximal and > distal to the regions of interest, however, as far as I know the BACs have > not been fully sequenced. I have some questions: > The end reads are available for each BAC, is the "between" sequence available? > I'm trying to find orthologous regions in human compared to dog and in some > cases, the regions span a breakpoint in synteny between the species. > According to the Ensembl synteny feature, I have a general idea of which > parts of dog chromosomes are orthologous to which parts of human chromosomes. > However, I'm not sure how to identify specific coordinates for the > breakpoint in synteny. > Thanks for any help you can provide! > > > > > Shannon Becker > [email protected] > PhD candidate > Comparative Biomedical Sciences > College of Veterinary Medicine > North Carolina State University > > http://publicationslist.org/shannon.becker > http://www.breenlab.org > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
