[Bioperl-l] Proteins in Compara

Ewan Birney birney@ebi.ac.uk
Thu, 7 Mar 2002 09:26:14 +0000 (GMT)

On Thu, 7 Mar 2002, Elia Stupka wrote:

> I am looking at the new Protein objects we have in compara and realise
> that depending on the stage of the process we want them to behave as
> different things:
> 1)PrimarySeqI compliant objects with lazy sequence fetching (sort of like
> DBPrimarySeq in Ensembl)
> 2)SeqFeatureI compliant objects that sit on genomic DNA, have starts and
> ends on it,etc.
> To stick to practical needs rather than design dreams, it is true that we
> really need the start and end, and not the underlying sequence, but I can
> imagine eventually we might want it...
> Assuming one could split the problem, and pull out the genomic DNA as a
> PrimarySeqI object, and the Protein as a SeqFeatureI object, there is
> still a problem in that the Protein should give out an AA sequence, not as
> a result of a translated DNA, but as "its own"....

Hmmm. The problem here is that SeqFeatureI and PrimarySeqI both define the
method seq which has different semantics.

I would go for a simple break of classes as follows:

  GenomeProteinLocation   ---> isa Bio::SeqFeatureI

  Protein                 ---> isa Bio::PrimarySeqI

Of course ideally you want to have a two way link (from Protein --->
GenomeProteinLocation, visa versa) but due to !"$""$"!!1 Perl's
memory management, you'll have to make that a spiral (assumming both are
database aware). Spiral don't cost that much as the number of times a
piece of code really spirals is minimal and you should be able to cache
things in the adaptor if necessary....

Does this make sense?

> What do people think is the best way to deal with it? Is there any elegant
> way, or should we just roll out a PrimarySeqI compliant object that
> "happens to have" another PrimarySeqI attached to it, and a start and an
> end? Yuck....
> Ah, uh, wait a sec, what about locatable seq? Is that any good?

I don't think that is useful...

> Elia
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420