Dear Qing, The Mouse Chain/Net track on the hg18 assembly displays the orthologous regions that you are looking for.
Here is the description page for this track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chrX&g=chainNetMm9 The subtrack that would be relevant is the net track. The table browser is the tool that you will want to use to extract this information. In the blue navigation at the top of the page click on "Tables". Set the following: clade: Mammal genome: Human genome: hg18 group: Comparative Genomics track: Mouse Chain/Net table: Mouse Net region: genome output format: selected fields from primary and related tables If you want the output to go to a file you will need to specify a file name: output file: FileName Click on "get output" Check the items that you want displayed in your output such as: tName Target chromosome tStart Start on target tEnd End on target strand Orientation of query. + or - Click on "get output" Hope this helps. If you have further questions, please don't hesitate to contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Qing Song" <[email protected]> To: [email protected] Cc: [email protected] Sent: Thursday, September 9, 2010 4:04:07 PM GMT -08:00 US/Canada Pacific Subject: [Genome-mirror] Whole Genome Orthology Map My question is - do you have the Whole Genome Orthology Map/datasets between human and mouse in your database that I can download? I want to have a dataset that can tell my software which chromosome region (not genes) in human corresponds to which chromosome region in mouse. I know JAX has one, but it is gene based rather than region/position-based and I have not found how to download the entire dataset. Thank you. Qing Qing Song, MD PhD Assistant Professor Cardiovascular Research Institute Morehouse School of Medicine 720 Westview Dr SW Atlanta, GA 30310 Phone: 404-752-1845 Fax: 404-752-1042 Email: [email protected]<mailto:[email protected]> _______________________________________________ Genome-mirror mailing list [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
