I have asked the following question on the gmod-gbrowse list without reply. I would have expected this an extremely common task, but seemingly it's not implemented. Any ideas? Note, I'm referring specifically to GBrowse or Tripal, sure we can get the spliced sequence (e.g. Extract Cds Fastas From A Gff Annotation + Reference Sequence ) but I need a user-friendly solution which is embedded into Gbrowse or Tripal and accessible via the web interface of those.
Some of our users need to export only the spliced mRNA sequence or CDS sequence for designing primers.
Is there a simple way or configuration option or plugin which allows to export spliced sequences? I think that there should be an easy way, if I use the protein sequence dumper plugin, I get the identical protein sequence as predicted by maker for that gene model, so there should exist some correctly spliced coding sequence in an intermediate step.
We are using GBrowse 2.54 with a chado backend and Bio::DB::DAS adapter.