Hi Emmanuel, You may download the annotation database on our server by clicking on "Downloads" (from the main page, located in the left-side menu), or clicking here: http://hgdownload.cse.ucsc.edu/downloads.html. Select the organism of interest ('Human' for example), and you will be directed to all the download links for that organism. The Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) is also a useful tool for uploading chromosome locations and retrieving sequences, etc. Please refer to our help pages on how to use the Table Browser: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
I hope this helps. Also, please feel free to search the Genome mailing list archives by visiting our home page and clicking on "Contact Us" (http://genome.ucsc.edu/contacts.html), or email us again at [email protected] if you have any further questions. Regards, --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 8/23/2011 10:31 AM, Ojefua, Emmanuel wrote: > ---------------------------- Original Message ---------------------------- > Subject: Analysis! > From: "Emmanuel Ojefua" <[email protected]> > Date: Tue, August 23, 2011 11:29 am > To: [email protected] > -------------------------------------------------------------------------- > > Hi, > > I have a list of chromosomes and the specific regions I am interested in, > for example: Chr2: 132455556-132470031. I have a huge list of these and I > am trying to use PERL scripts to just extract these lines, and possibly > their corresponding sequences, and analysis for CpG islands, repeats, > promoters, etc. I really think my data is huge that I want to avoid > copy/paste in the genome browser. Just wondering if you have databases or > tools I could use and be able to directly use these tools inside my > script/program. What do you think is the best way for achieving this? > > Thanks, > Emmanuel Ojefua > Kovalchuk's Labs > Univeristy of Lethbridge, AB, Canada > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
