[Biojava-l] genes and things

[Matthew Pocock]

Hi Niclas - hope everything is going well with you.

Niclas Jareborg wrote:

> At 18.00 -0700 00-09-27, Ann Loraine wrote:
> >In general,
> >
> >       -A gene has 1 or more transcripts (due to alternate
> >               transcriptional start sites)
> >
> >       -A transcript has 1 or more mRNA splice variants (due to
> >               alternative splicing)
>
> I agree that this makes biological sense. But, does it make sense
> "modeling-wise"? Is there any advantage to destiguish between
> transcripts and splice variants? The way I think about it a gene has
> one or more 'mRNA products' that will have at least parts of exons in
> common (otherwise I'd call it two genes).
>
> -Nic

Bacterial (and C.Elegans) operons could be modeled as transcripts with with a set
of non-overlapping TranslatedRegion objects (or for c-elegans, SpliceVariants
with multiple TranslatedRegion thingys) - one per 'gene' . This kind of destroys
the meaning of the 'Gene' interface, though. Mabey the top-level thing is
ExpressedRegion (promoter stuff & transcripts), or Expresson, or Regulon or
something, and 'Gene' information is mixed in somewhere? Pants. I think for the
C.Elegans operons, we would end up using each level of the hierachy to add
information.

For bacterial genes, I guess we drop the splice-variant layer, or have a standard
view of each Transcript producing a default SpliceVariant that contains the whole
of itself.

Trans-splicing is a whole other tin of worms.

>
> --
> Niclas Jareborg, PhD                         Center for Genomics Research
> niclas.jareborg@cgr.ki.se                    Karolinska institutet
> http://www.cgr.ki.se/cgr/groups/jareborg     S-171 77 Stockholm, Sweden
> Tel:+46-8-728 69 20    Mob:+46-70-7630461    Fax:+46-8-337983
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