[Bioperl-l] Re: Another update for my alignment module

[Aaron J Mackey]

On Wed, 21 May 2003, Yee Man Chan wrote:

> > I think that the developers of vector and other parallel-processed
> > DP algorithms would disagree with it being the fastest.
> >
>
> Ok. I can clarify by adding it is for single CPU...

I would just prefer you not say that any current algorithm "is the
fastest", because it's bound to be wrong.

> > You've already said that the Phil Green optimized SW can't be used to
> > generate an alignment (which is untrue for the reason's I've already
> > given) - what does DPALIGN_LOCAL_GREEN do then?
>
> It means the search phase is using Phil Green's code. If his code can also
> do alignment, it will be a complete Phil Green local alignment algorithm.

We're talking about your package now, not SSEARCH; what search phase does
dpAlign have?  Your synopsis says that I can get a Bio::Align-compliant
object out of $factory->pairwise_alignment($s1, $s2) ... will I get an
alignment object if I initialize my factory with DPALIGN_LOCAL_GREEN ???

> I looks at the blosum62.mat file in FASTA. It doesn't have "*". Is the
> stop codon really an aa?

Well, B, Z and X aren't really amino acids either, but they show up in
protein sequences.  And if you translate a DNA sequence in all six frames
you'll quickly find some stop codons.

The blosum62.mat file in Bio/Ext/Align/ has a row for '*'.

-Aaron

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