Hello Suzanne, Unfortunately you will need to have an specific identifier for each marker whose sequence you wish to retrieve. Once you have this in hand you can use our Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) tool as follows. Select:
clade: Mammal genome: Human assembly: hg19 group: Mapping and Sequencing Tracks track: STS Markers table: stsMap then click on "filter: create". Scroll down to the "Linked Tables" section on the next page, check the box beside "stsAlias" and click "allow filtering using fields in checked tables". Now you should have a section titled "hg19.sts.Alias based filters". Input your identifiers (i.e. D2S123) as a space separated list (i.e. D2S123 AFM304XD5 Z16979 ... etc) in the "alias does match" box and hit submit. Now in the main Table Browser menu select: output format: sequence and click "get output" and select the sequence formatting options you prefer in the next menu. This should generate one fasta formatted sequence per identifier that you pasted into the filter. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 7/10/12 4:03 AM, SUZANNE E HILE wrote: > Hello!! > > I am currently working on a project in which I need > to determine the sequence of a long list of microsatellite markers that are > used > in cancer diagnostics. I have not found a database where this information is > readily available. For some markers, I have both the name (for example, > D2S123) > and its accession number and could find its sequence using UniSTS. For other > markers, I only have the common name and no accession number and am unable to > find a sequence. Still for other markers, I type in the common name and then > get many listings with different accession numbers. > > Is this information readily available using the UCSC genome browser? If so, > how do I find it? Do I need to find the accession numbers for all of my > markers > before I begin to look for their sequences and if so, where do I > find that information? > > I really appreciate any suggestions and thank you > so much for your time! > > Suzanne Hile > > Penn State College of Medicine > Gittlen Cancer Foundation > 500 University Dr. > Hershey, PA 17033 > > (717) 531-4132 > > > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
