Looking for a plugin exporting spliced sequence from GBrowse or Tripal.

Question

[Michael]

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.

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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.

[SES]

I don't think this exists but it would be a great feature to have. I recently tried to export the CDS for a gene and found that I had to use a script for the task even though the CDS are displayed when you click on the sequence features.

Answer 1

[Michael]

The solution was right in front of my eyes, simply take away the translation part from ProteinDumper.pm. Changed also slightly the way the header is generated. I simply trust that the collection of CDS' was correct before. Added a PlugIn on github: https://github.com/mdondrup/GBrowse/blob/master/conf/plugins/CdsDumper.pm

To use, put the Plugin into your gbrowse plugins directory, add

plugins     =  [other plugins]  CdsDumper

to your config and restart. Select a region and get an export like this:

>EMLSAG00000001234 gene, complete CDS, Predicted by MAKER 424821..428389 +
ATGAGC...

​Hope this is useful. I thought I could add options for sequence features of other type, like "spliced mRNA", "UTRs only", "introns only".