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

[Hilmar Lapp]

On Wednesday, September 4, 2002, at 10:00  AM, Aaron J Mackey wrote:

>
> 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?

Absolutely not. That's why I suggested this. If you look at my 
implementations of the cds() methods there's a lot of hard-coded 
guesswork if exons don't plug into each other as nicely as they 
should. Using such an encoding would not do away with that 
guesswork, but offers the client (or constructing class) a chance to 
change or preset the result of that, which I think is going to be 
very useful.

	-hilmar

>
> 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
>
>
--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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