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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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View details panel for loaded gene predictions does not show peptide sequence #732

Open strumpfe opened 8 years ago

strumpfe commented 8 years ago

Existing gene predictions loaded into WebApollo as a track have the 'View details' option. This opens a new popup window which contains more information about that prediction. Specifically it displays the nucleotide sequence for the transcript and each exon. It does not however show the peptide sequence for the CDS.

Attempting comparative annotation across similar species (e.g. 19 Anopheles) I sometimes find myself with less than perfect evidence tracks and can only correct/manipulate some predictions by looking for small amino-acid sequences. This involves a certain amount of multiple-sequence alignments (clustal) outside of Web Apollo but I find myself wanting to know/access the peptide sequences for loci in our canonical gene set track. I do this by promoting the prediction into the user-created annotations and use the 'Get sequence' functionality. Once I have finished I delete the annotation. This is not an efficient way to access the peptide translation of the CDS.

annotation_details_lacks_peptide_sequence

nathandunn commented 8 years ago

I really like this idea and agree that the current workflow seems un-necessary.

What I'm unsure of is if doing this through JBrowse or Apollo makes the most sense. There is some functionality in JBrowse that we can leverage but I'm not sure what the best method would be. @enuggetry or @cmdcolin might know better.