[Bioperl-l] Re: Frameshifts in alignments ... ?

[Aaron J Mackey]

On Wed, 4 Sep 2002, Hilmar Lapp wrote:

> Wouldn't we want the Transcript and Exon classes to utilize this too
> for the cds() method, or is something in this mechanism that makes
> it specific to alignments?

I would think that Transcript and Exon classes would be built using these
things ... do you see anythign wrong with that?

I didn't think that Bio::EncodedSeq had anything to do necessarily with
alignments (just as Bio::LocatableSeq doesn't), but I envision them as
being useful in an alignment context (just as LocatableSeq is).

-Aaron