Re: [Gusdev-gusdev] Re: GUS 3.0 schema changes: ASCII art redux

[Arnaud K. <ax...@sa...>]

Hi Jonathan

Quoting Jonathan Crabtree <cra...@pc...>:
> 
> Arnaud-
> 
> Returning to some slightly older business...
> 
> >>
> >>                           <DoTS::GenomicSequence>
> >>                           ^      ^      ^    ^  ^
> >>                           |      |      |    |  |
> >>     <DoTS::GeneFeature (RHS)>    |      |    |  |
> >>               ^                  |      |    |  |
> >>               |                  |      |    |  |
> >>    <DoTS::TransposableElement (INGI)>   |    |  |
> >>    ^                ^                   |    |  |
> >>    |                |                   |    |  |
> >>    |           <DoTS::RepeatRegionNAFeature> |  |
> >>    |                   ^                     |  |
> >>    |                   |                     |  |
> >>    |          2 x <DoTS::RepeatFeature (RIME)>  |
> >>    |                                            |
> >>    |                                            |
> >>    ------------------------<DoTS::GeneFeature (pseudo)>
> >>
> > 
> > My proposal is this representation without the repeat region feature. I
> would
> > see the repeat region feature to cluster together a sequence, whatever
> the
> > sequence is (even one base, or more), repeated X times, but not being used
> in
> > this situation.
> 
> Meaning that you would only use the repeat region feature when X > 1,
> right?

yes

> I'm suggesting that we combine the two tables, meaning that we would have
> one
> uniform representation for all X.  I suppose that's probably my strongest
> argument against the 2-table representation, namely that it seems arbitrary
> to say that something is only a "repeat region" when it contains > 1 copy
> of
> a repeat.  Wouldn't such a thing be better described as a tandem repeat?

Yes I guess it could as a repeat region was meant to annotate tandemly repeated
DNA sequences. I can see a TandemRepeatFeature in GUS very similar to the
proposed RepeatRegionFeature. Are you planning to keep it in replacment of the
RepeatRegionNAFeature ?

> >>region".  Specifically, can a repeat region contain things that are not
> >>repeats,
> >  
> > Yes ! a gene for example !! A repeat region would be used to cluster
> tandemly
> > repeated genes. But this should be fine as long as a gene feature can be
> > attached to a repeat region.
> 
> My question wasn't quite correct; I should have asked whether a repeat
> region
> can contain things that are not repeated.  That is, could you use a repeat
> region
> to cluster tandemly repeated genes if those genes were separated by some
> additional non-repeating sequences.  It sounds like the answer is probably
> "yes",

I think so.

> and that your definition of repeat region is simply any region that contains
> two
> or more copies of some type of sequence.  Is this accurate?
 
yes

> > I think we want to represent a transposable element in a given context, ie
> at a
> > given location because this insertion may have consequences, (in)activating
> a
> > gene or shifting the frame of a gene etc.
> > 
> > A core transposon should be represented as an entity on its own like genes
> are.
> 
> OK, I agree, and I think that fits with the current schema (except that we
> have
> yet to create a table to represent the transposons independent of their
> location.)

ok, I guess this can wait. I reckon that would involve that the Central Dogma
side would not only represent genes, right ?
 
> Jonathan
> 
> -- 
> Jonathan Crabtree
> Center for Bioinformatics, University of Pennsylvania
> 1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
> 215-573-3115
> 
> 

Arnaud