Hi Jennifer, My apologies - when I tested this I didn't check that the chromosome coordinates were exactly the same. Sorry for misleading you. In the process of researching this further I found a FAQ that answers your question exactly: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download32. Essentially you will create a custom track (http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks) of the genomic coordinates in a BED format and upload this to the Genome Browser. Then select the custom track in the Table browser and select "sequence" as the output format to retrieve the data.
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 11:47 AM, Barb, Jennifer (NIH/CIT) [E] wrote: > Hi Mary, > This information has been very helpful however I am a little confused. I > entered in some coordinates, such as: > chr12 119368666 119368747 > > and what is returned to me is DNA with the following coordinates: > > >> hg18_gold_AL021546.1 range=chr12:119343491-119399640 5'pad=0 3'pad=0 >> strand=+ repeatMasking=none >> > Can you explain to me what the browser is doing? I thought that I could > obtain the DNA for a specified range and get the sequence back for only that > range. Is this not possible? > > Thank you again for all of your help. > > Sincerely, > Jennifer > > > -----Original Message----- > From: Mary Goldman [mailto:[email protected]] > Sent: Monday, July 19, 2010 1:46 PM > To: Barb, Jennifer (NIH/CIT) [E] > Cc: [email protected] > Subject: Re: [Genome] Fasta sequence from genomic coordinates > > 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
