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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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Get sequence with exons/introns marked #1854

Open AlanTracey99 opened 6 years ago

AlanTracey99 commented 6 years ago

Hi

I want to get sequence for my gene, including the introns. Currently, I can see that 'genomic sequence' gives me this, but it would be really nice to have the introns/exons highlighted - maybe lower case for introns and upper for exons? Below is an example where I've annotated the CDS portion of my gene using upper case and the UTRs and introns are lower case. I think this would be a useful feature.

image

nathandunn commented 6 years ago

From JBrowse already:

  1. FeatureSequence (https://github.com/tsaari88/FeatureSequence)
  2. SeqLighter (https://github.com/Arabidopsis-Information-Portal/SeqLighter)
nathandunn commented 6 years ago

@AlanTracey99 would the plugins above work with the Annotation Track?

AlanTracey99 commented 6 years ago

Sorry for delay in replying. I think this would be good if implemented for the annotation area.