Hello Oranit, The Custom track feature along with the Table browser can help identify this type of data. There is also a PCR tool that you may find helpful.
Gene tracks are located in the "Gene and Gene Prediction" track grouping. Start with UCSC Genes to locate your genes and move to other tracks as needed. You can even BLAT a sequence against the genomic (if it is not in the Browser) and save a custom track to view against the other data in the Assembly browser. For any dataset, the track description page lists methods, credits, and has links to the base tables that contain the data, linked to the Table browser. Once you are familiar with the gene tracks, go to the Table browser, set the variables and enter a list of the gene identifiers to limit output. One output option is "sequence" where you can specify predicted promoter regions based on upstream DNA. Save the data as a custom track. Also saving the complete table data may be interesting you. Notice that for many tracks, the base table has links to other tables that can be joined into the output. To identify CpG islands that contain the regions in the custom track of promoters (above), set the Table browser variables for the track "CpG Islands" in the "Regulation" track grouping. Use the intersection feature to limit the output from the CpG Islands track to be only those regions in the custom track created above. Save again as another custom track or download. Use the Assembly browser to view details, locate regions for primers, etc. The "get DNA" tool (DNA link in top blue bar) can extract sequence for any genomic region. Try using the Sessions feature to increase the amount of time that custom track data can be saved on the server (but keep downloaded back-ups!). Some links for help: http://genome.ucsc.edu/cgi-bin/hgTables http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://genome.ucsc.edu/cgi-bin/hgCustom http://genome.ucsc.edu/FAQ/FAQcustom http://genome.ucsc.edu/cgi-bin/hgPcr http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html http://genome.ucsc.edu/cgi-bin/hgSession For sample queries on related topics, a search against the mailing list archives may be informative: http://genome.ucsc.edu/contacts.html This should help you to get started, Jennifer Jackson UCSC Genome Bioinformatics Group oranit zadok wrote: > hi > > my name is oranit and im doing a research about epigenetic changes in lung > cancer. > > I want to use the UCSC Genome Browser for detection of promoters and their > CpG islands- can you explain me how to do so? can you also explain how can I > design primers for CpG regions of the genes im interested in? can you give > me the general guidelines? > it is very urgent and i will appreciate the answer... > > thank you in advance, Oranit > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
