Hello, There are a few choices:
1) Retrieve the data via ftp from the Downloads server and create your own scripts to parse out the data. http://hgdownload.cse.ucsc.edu/downloads.html 2) Open up the Conservation track and use the track filters there to view results. Perhaps save as a Session. http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Sessions 3) Use the Table browser to filter the data (will not be exactly what you specify) and download or save the results as a custom track. http://genome.ucsc.edu/cgi-bin/hgTables 4) Use the Public mySQL server to create a custom filter with your own scripts to parse out the data. http://genome.ucsc.edu/FAQ/FAQdownloads#download29 If you are still unsure, the best place to start is with #2. View the data and learn about how it was created/organized. From there are links to the Table browser files that contain the data. Files in downloads are organized by the database and track name. The mySQL table names == file names. Good luck and please let us know if you need more help, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Robert Cornell" <[email protected]> wrote: > From: "Robert Cornell" <[email protected]> > To: [email protected] > Sent: Friday, September 11, 2009 11:02:34 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] assessing conservation > > I would like to scan genomic DNA for regions of a given size, say 100 > > bp, with a given degree of conservation, say 50% identity at the > nucleotide level, among a given set of species, say mammals. How do > > I do this? I know it has something to do with PhastCons, but that's > > about it! > > Thank you! > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
