[Bioperl-l] Framshifts in alignments ... ?

[Aaron J Mackey]

On Thu, 29 Aug 2002, Ewan Birney wrote:

>   (b) there is no bioperl alignment model which sensibly handles
> frameshifts

What is the consensus on this issue?  We've just made the FASTA programs
output using -m 9c horribly trivial to parse the alignments (we dump a
coded string of gaps and frameshifts, after which you can easily grab the
sequences from the alignment display, strip any gap/frameshift characters
in it, and use the coded string to reconstruct from scratch; much much
easier than parsing out the alignment).  We're working on making
Search::IO::fasta -m 9 "capable", and it'd be great if we could start
throwing alignment events as well ...

-Aaron

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