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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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Potential new functionality for the 'Get sequence' popup panel #736

Open strumpfe opened 8 years ago

strumpfe commented 8 years ago

The 'Get sequence' menu option opens a window with the peptide sequence displayed as default. I have two suggestions to augment this based on what I operationally do when annotating (1000s of loci).

Firstly, finding exon boundaries is important when checking and refining predictions, especially where evidence is sparse (e.g. comparative alignments across 19 Anopheles spp. for those that do not have RNAseq). In VectorBase we colour the peptide sequence for alternating exons such that the boundaries are clearly visible (though I don't find black/blue personally easy).

alternating_exon_colouration

Secondly, often once I have a prediction completed (e.g. think a merge of two incorrectly predicted loci) I like to check the alignment against nr at NCBI. This involves the cut-n-paste of the peptide sequence into the blastp server at NCBI. It is possible to pre-load this page via webservice so how about having a button in the popup panel which is configured to initiate the blastp against nr? This would save me a lot of time and I would suggest is something most users should be doing before signing off on a prediction. In fact having a clear icon/button may encourage people to do so and may even increase the veracity of people's predictions.

user_annotation_show_sequence_window

nathandunn commented 8 years ago

I think that both of these are great features. We've talked about the remote blast one, though it would take some though. I'm kind of surprised that no one has asked about coloring the sequences that come back though. It just makes sense.