Dear Dr. Mary, Could you please tell me how to annotate some sequences, and get the information which gene this sequence belongs to? I only have sequences physical start/end positions, and don't have ATCG sequence information, the sequence length could be short (eg.40bp) or long(2000bp).
There are more than 500 sequences need to be annotated, so can I use UCSC Genome Brower or Galaxy to perform annotation for a large number of sequence at one time? Thanks very much. Your Sincerely, Joshua. On Tue, Sep 28, 2010 at 12:36 PM, Mary Goldman <[email protected]> wrote: > Hi Joshua, > > The easiest way to download all the CpG Islands with their coordinates and > names is to use the table browser (http://genome.ucsc.edu/cgi-bin/hgTables). > First, select the clade, genome and assembly of interest. Next, select > "Regulation" from the group pull-down menu and "CpG Islands" from the track > pull-down menu. Select "selected fields from primary and related tables" as > the output format, enter a name for the output file if you would like (leave > blank to keep output in browser), and click "get output". Select the > "chrom", "chromStart", "chromEnd" and "name" check boxes and click "get > output". > > I hope this information is helpful. Please feel free to contact the mail > list again if you require further assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > > On 9/27/10 9:07 PM, qcshare wrote: > >> Dear Professor, >> I want to download the genome CpG islands information, such as the number >> of >> chromosome, start/end position of the CpG islands and CpG islands ID >> numbers, I just found the first three items, but I can not found the >> information of CpG islands ID numbers. >> Could you please tell me where can I get this information? >> >> Thank you very much! >> >> Your Sincerely! >> >> Joshua. >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
