[Bioperl-l] 'virtual' seqs

[Elia Stupka]

> IMHO the connotation of UnknownSequence is overloaded too (refering to
> a sequence for which there is no functional annotation, or which
> hasn't been characterized experimentally yet). It appears that
> VirtualSeq has some consensus ... even though I recall someone (Elia?)
> saying that's too overloaded either.

I do think that VirtualSeq (not only in Ensembl) is often used to indicate
a virtual *longer* sequence made by pulling together an assembly of
sequences.

The term Lazy really has to do with lazy fetching and nothing to do with
an empty sequence.

I still think EmptySeq is the simplest way to call something that we are
all referring to as an empty sequence.... ;) but I don't really see why it
should return NNNs... it is not meant to be storable with a sequence. In
other words there is a good reason why EmptySeq->seq should return undef,
and that is that it is not meant to be filled with a sequence, and thus
no sequence is meant to be stored...

I totally agree with Hilmar, we have tons of fully masked sequences, which
are all made of NNNs... as well as gaps,etc. all made of NNNs, it really
is not the same thing as an EmptySeq...

Elia

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