Hi Jennifer, Use our Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) to get DNA for several coordinates. First select your species and assembly of interest. Next, select all "All Tables" from the group pull-down menu and then "gold" from the table pull-down menu (gold is the base track). Click on the "define regions" button at the end of the line starting with "region". This will take you to a page where you can paste in your coordinates. Finally, select "sequence: from the "output format" drop-down menu 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 7/19/10 6:49 AM, Barb, Jennifer (NIH/CIT) [E] wrote: > Hi Mary, > Thank you for your response. I am wondering however, if there is a way to do > this in batch mode for a list of genomic coordinates? > Thank you, > Jennifer > > > -----Original Message----- > From: Mary Goldman [mailto:[email protected]] > Sent: Thursday, July 15, 2010 5:56 PM > To: Barb, Jennifer (NIH/CIT) [E] > Cc: [email protected] > Subject: Re: [Genome] Fasta sequence from genomic coordinates > > Hi Jennifer, > > We recommend using the "DNA" button in the top blue bar when you are > viewing your assembly of interest. This example link is for hg19, > chr21:33,031,597-33,041,570: > http://genome.ucsc.edu/cgi-bin/hgc?g=getDna&i=mixed&c=chr21&l=33031596&r=33041570&db=hg19. > > 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 7/15/10 11:31 AM, Barb, Jennifer (NIH/CIT) [E] wrote: > >> Hello, >> Does anyone know of a tool that will allow you to upload genomic coordinates >> (ie. chrom, sequence start, sequence stop) and can get back the fasta dna >> sequence of those coordinates?? >> >> Any information would be incredibly helpful. >> Thank you, >> Jennifer Barb >> >> ------------------------------------------------------------------------------ >> Jennifer J. Barb, Ph.D. >> Mathematical and Statistical Computing Lab >> Division of Computational Biosciences, CIT/NIH >> Bldg12A, Room 2001, Bethesda, MD 20892 >> 301.435.9232, (fax) 301.480.0028 >> [email protected] >> ------------------------------------------------------------------------------- >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
