Hello Kumaran, To be clear, the current dbSNP data is mapped by dbSNP. For other data, the utility "LiftOver" is used along with a mapping file to move data between assemblies for the same species and sometimes between distinct species.
LiftOver is in the browser as a web utility, in the kent source tree where you can compile it locally, or on the downloads server pre-compiled for some systems. The inputs for liftOver are the coordinates for the track being lifted and an "over.chain" file mapping one genome to the other. Browser utility: http://genome.ucsc.edu/cgi-bin/hgLiftOver Complete source and compiled utility: http://hgdownload.cse.ucsc.edu/downloads.html Scroll to -> Source Downloads Source tree map: http://genomewiki.ucsc.edu/index.php/The_source_tree The "over.chain" files are also located on the download server, organized under species -> assembly -> "LiftOver files". Files in most cases are under the "from" assembly. For example, the "over.chain" file for converting "from hg18" "to hg19" is named hg18ToHg19.over.chain.gz and is located here: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/ Downloading through a browser is not recommended, please follow the ftp instructions in the link above. LiftOver has many options. You will need to experiment with these to get the best results for your particular dataset. Type the program name at the command prompt for the usage. The usage is also listed on this page along with other comment kent source tree utilities (a temporary link, not a permanent Help document): http://hgwdev.cse.ucsc.edu/~larrym/utilities.html Scroll to liftOver Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/27/10 6:20 AM, Kumaran Kandasamy wrote: > Dear UCSC Genome browser team, > > We have mutation data from published studies that are mapped to a > older build of human genome. Can you please let us know the method > for mapping this mutation sites to the current genome build? It would > be great if you can let us know how you map the SNP data when you > update the genome build. > > Best regards, > > Kumaran > > Kumaran Kandasamy > Ph.D. Student > McKusick-Nathans Institute of Genetic Medicine > Pandey Lab (<http://pandeylab.igm.jhmi.edu/>http://pandeylab.igm.jhmi.edu/) > Johns Hopkins University > Broadway Research Building, Room 560 > Baltimore, MD 21205 > Phone: 410-502-3194 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
