[Bioperl-l] Proteins in Compara

Elia Stupka elia@fugu-sg.org
Thu, 7 Mar 2002 15:11:38 +0800 (SGT)

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"....

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?


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