[Jalview-discuss] Representing Exon boundaries

[James Procter]

Hi Lars..

Lars Arvestad wrote:
> I am glad this topic comes up because it is something I have done more
> or less by hand in a couple of cases, and it is inconvenient.
> 
> However, I just want to point out that exon boundaries can occur within
> codons, so it is not straightforward to represent it on the amino acid
> level. In fact, it is not obvious how to visualize it.

Very good point. I suspect there are one or two different conventions,
in fact. With regards to handling the underlying data, within the VAMSAS
datamodel we explicitly built in the concept of annotation being either
at a discrete position (i.e. base or residue) in a coordinate system, or
after it, in order to properly reflect inclusive or exclusive
boundaries. I think it might be possible to utilise the same trick for
proteins. Codon boundaries are at a residue, or after it. Anything more
would have to be a subtype.  Of course, the original issue stands -
jalview won't render exon boundaries  after a residue. It could,
however, be 'hacked' in as a special feature representation:
'disulphide' feature type rendering is done this way.. ( as a hack - but
in principle, the rendering model could re-implemented as something more
generic that is driven by some ontology/look up table of feature types
and styles). One could almost imagine positioning a bar either mid-left,
mid-right, or at the right of the residue symbol.

j.


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