[Jalview-discuss] Representing Exon boundaries

[James Procter]

Hello Albert.

Albert Vilella wrote:
> Is there any formal way to represent exon boundaries in a protein
> alignment in Jalview?
Actually, no. There is support for this kind of annotation internally,
but it is currently only used for the linked highlighting of DNA and
protein views, and mapping features and annotation.

I have also noticed cases in the literature where exon boundaries have
been added to an alignment as vertical bars, and at the time realised
that it would be useful to do this. I guess it would be possible to mock
up the annotation by creating a group on the sequence for each exon
region on the peptide product - but this is pretty painful to do by
hand, and would be alignment annotation - rather than sequence
annotation, so would be broken as soon as the alignment was edited.

This will be a good addition to the jalview feature list - no guarantees
about when it is done .. of course.. but perhaps sometime soon (unless
there are any volunteers!).

thanks.
Jim

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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
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