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Old 12-01-2014, 02:26 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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The simplest thing is to probably use blast to align them to you either the genome or the targeted region and then use some of the replies in this thread over at Biostars to convert that to GFF/GTF. I should note that I've not personally done this, so I can't say how easy/difficult it is...but it should at least work well in theory (famous last words!).
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