[Bioperl-l] Re: Gene Interfaces in Bioperl 0.7; Review of bioperl 0.7 from Ensembl

[Lukasz Huminiecki]

Ewan, Hilmar,

How to decide on the size of a promoter? Certainly, it ends at a 
transcript starting point, but where does it start? It's hard to be
certain where biologically active elements are. For most wet-labs, it
would be 'as much as we have cloned', really.

For genes, in contrast to transcripts, there could be, of course, multiple
promoter end-points as well. For example, dystrophin and utrophin (Kay
Davies, Oxford) are known to have multiple starting points. Some
transcripts have different tissue-specificty; utrophin normally expressed
in muscle/neuronal junctions seems to have an endothelial-specific
transcript (!?).

Cheers, 

Lukasz
(Hi, I am a new member of the ENSEMBL team!)

> 
> 
> 
> Hilmar -
> 
> I like the interfaces. They are quite feature-rich but that does make
> them useful. 
> 
> My only comment is that I would expect 
> 
> $transcript->promoter 
> 
> to return a single object. A transcript is, in my view, defined to have a
> single promoter (ie, there is one unique starting point in the DNA). Of
> course, this really depends what on earth is "a promoter" --- which we are
> punting on right?
> 
>  
> 
> 
> 
> This model works very well with Ensembl. Once bioperl-0.7 is out and
> stable we should be able to be compatabile  with it very quickly.
> 
> The only challenge here is implementing aspects of the SeqFeature
> interface on our gene/transcript objects, which prefer to be "location
> -less". This is ok in our new world of rich locations - it is just a
> challenge to implement.
> 
> 
> (one for Arne - it is like when we get Genes/Transcripts out from the
> database currently they have *no context* in a location sense. Only their
> exons have a context. The bioperl Gene/Transcript interfaces require a
> gene to have a context, being start/end/strand/seqname so we have to dream
> up what we can do here. Easiest fix is that context is the implied context
> from the start-codon-exon.)
> 
> 
> Re: Ensembl <-> Bioperl 0.7
> 
> I am pleased to say that with only one addition I was able to get Ensembl
> to pass its entire test suite (390 tests) against Bioperl-live /0.7
> candidate
> 
> I got alot of "deprecated object" noise etc etc...
> 
> I think that is a real tribute to Hilmar and Jason providing excellent
> backward compatability for bioperl. We are indebted to you two guys.
> 
> 
> 
> ewan
> 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
> 
>