Hi Yang, We recommend that you take a look at the "Human Proteins" track and the "TransMap" track for the dog assembly. To get more information click on the the links for the tracks from the dog browser.
Hope this leads you in the right direction! If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Yang Shao" <[email protected]> To: [email protected] Sent: Wednesday, April 27, 2011 2:05:32 PM Subject: [Genome] Dog to human mapping Dear all, Our lab have done some aCGH on dog cancer and we were able to identify a few regions, we are interested in finding out what genes are there in these regions . However, the dog genome is poorly annotated (only around 1300 genes have been annotated). So my idea is to convert the dog genome regions into ortholog human regions and find out what genes are there in those human regions. This way is not 100% accurate, but I am guessing 80-90% of the time it does the right job. I am using the liftover tool from UCSC genome browser (CanFam2 to Hg19). If I set the "Minimum ratio of bases that must remap" to 0.8, about 30% of the dog regions can remap into human, and if I set the number to 0.5, about 80% of the regions can remap. So my first question is "Is 0.5 considered too loose of a criteria"? Also, if I allow "multiple regions", more regions are able to remap. But the output are extremely fragmented (I went from 22regions, average size of 100kb to 400 regions, average size of 0.5-2kb). The sum of the size of the regions also went from 11.5mb to 0.34mb. So I lost most of the regions somehow. Overall, I decided to go with "does NOT allow multiple regions". Another thought I have is some of dog regions are big (over 1mb), if I chop one big regions into 10 small regions (i.e. 10 regions around 100kb each), would it help the "liftover tool" to remap more precisely? And if I were to do this, what size should I start with? My overall goal is to find out what genes are there in these dog regions. Can you please let me know if I am on the right track, or maybe there is a better way of approaching the problem? Thank you so much for your time and effort! Cheers Washington _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
