[Jalview-discuss] Representing Exon boundaries

[Lars Arvestad]

Hi,
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.

    Lars,
    a happy Jalview user



James Procter wrote:
> 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
>
>   


-- 
Stockholm Bioinformatics Center
and School of Computer Science and Communication
http://www.csc.kth.se/~arve