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

[Aaron J Mackey]

On Tue, 3 Sep 2002, Ewan Birney wrote:

> > There was also my "embedded" encoding (which is what we tend to see in
> > alignment outputs), with frameshift (/, \), intron boundaries ([...]) and
> > gap characters, that I proposed could be obtained via as_string():
> >
> > ATGGGT/GTATG[TATTGTGTAAAAAG]AATGT\TAAGGTTGT---GTET
> >
>
> I think this is slightly insane (myself) as your coordinate system now has
> to keep track of lots of hting - of course, it has to keep track of gaps
> anyway. HMMM,.,,

Aha, you see we're talking about apples and oranges; I never meant that I
wanted to use this representation to compute on; only as an import/export
"format", this one being slightly more human readable, and better Huffman
coded.  Which led me to my next statement:

> > I guess now I'm inching towards an Bio::SeqIO::encoded::wise,
> > Bio::SeqIO::encoded::tfastx, ... ?

Which was all about "how do you want to build these things, given that you
have a formatted encoding of it already, provided by GeneWise, FASTX,
etc".

-Aaron

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu