[Bioperl-l] pI and MW of seqs

[Aaron J Mackey]

one of the small changes to bioSQL that we're proposing is to add pI and
MW columns to biosequences ... this lead naturally to thinking about how
we handle these attributes in the various Bio::Seq objects.  We've
previously batted around various Bio::Tools::pICalculator interfaces, but
what about a simpler:

$seq = <get seq somehow>;

$pI = $seq->pI();
$MW = $seq->MW();

where the pI and MW subs would see if the value had been already set (via
database load, or previously set/calculated) or needs to be calculated.

I think I prefer this to:

$calc = new Bio::Tools::pICalculator;
$pI = $calc->pI($seq);

Does anyone with a deeper understanding of proteomics want to comment on
the need to handle varying pIcalc parameters (e.g. different tables of
pKa's vs. the canonical one Expasy uses?)

-Aaron

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