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Old 04-03-2012, 04:24 PM   #1
Location: Cupertino, CA

Join Date: Nov 2011
Posts: 59
Default Query Ensemble or USCS

Is there any automated way to get DNA sequences from UCSC genome browser or Ensemble for a list of chromosomal coordinates of interest.

I have several chromosomal coordinates sets and cannot do it manually.

Thanks in advance.
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Old 04-04-2012, 03:28 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

If you have a bunch of ranges, then it might be most straight forward to just download the genomes in fasta format and just write a quick parser (samtools provides an fai_fetch function in the C API that can be given a genomic range and will return the sequence).
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Old 04-04-2012, 06:30 AM   #3
Senior Member
Location: Kansas City

Join Date: Mar 2008
Posts: 197

At UCSC, you can upload a custom track bed file, then use the table browser and do an intersection. You could also do this with galaxy "Fetch Sequences".

On the command line, you have a number of options... bedtools getfasta comes to mind.
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