[ensembl-dev] Mapping genomic coordinates to CDS

Jason Rozick jrozick at yahoo.com
Tue Nov 17 19:14:59 GMT 2015


You can see what introns are removed, and look at the remaining exons of mrna.  The border's base sequence of splice junctions are important, and how much you pad and track a search sequence during an event comparison.  


     On Thursday, November 5, 2015 12:00 PM, Greg Slodkowicz <gregs at ebi.ac.uk> wrote:
   

 Dear all,I'm working with a large (>500K) dataset of cancer mutations, all of which fall in coding regions. In the format I was given, the mutated positions are given as genomic (rather than CDS) coordinates. I noticed that the Ensembl REST API has a feature to map from protein to genomic coordinates (http://rest.ensembl.org/documentation/info/assembly_translation) but apparently not the other way round. What would be the simplest way to perform this kind of mapping?
Many thanks,
Greg
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