Re: [Gmod-ajax] jbrowse and the canonical gene

[Mitch S. <mit...@be...>]

James Casbon wrote:
> No, I just queried the GFF3 spec and apparently the canonical gene is correct.
>
> jbrowse's rendering could be considered correct as the glyph does span
> the entire feature.  I'm not sure it couldn't be improved though by
> actually showing the component blocks in the same way as subfeatures.
>   

I talked about this on the GMOD teleconference on Monday, and learned 
about BioPerl's SeqFeatureI::location mechanism that allows a single 
feature to have a location with multiple discontinuous spans.  JBrowse 
should probably support this, but unfortunately it currently doesn't.

The work-around at the moment would be to model your CDS segments as 
individual subfeatures, with different (or no) IDs and a Parent 
attribute pointing to the transcript.

So far in my testing, I've mainly encountered situations where people 
were doing that (modeling CDS segments as multiple subfeatures rather 
than a single feature with multiple locations).  I'd be interested to 
know if people reading this typically encounter one approach or the 
other, and whether y'all have strong opinions about this one way or the 
other.

Sorry about that,
Mitch