[Bioperl-l] pI and MW of seqs

[Brian Osborne]

Aaron,

Don't we want something more flexible, like:

$seq->property(-name=>"pI")

?

Arguments, using the pICalculator example, would be allowed:

$seq->property( -name=>"pI", -args=>\%hash )

where:

%hash = ( "pKset", \%pKset )

This implies a database table, something like Biosequence_Property, 
whose functionality
is essentially the fields Biosequence_Property.Property_name and 
Biosequence_Property.Property_Value.
Presumably Property_Value is a floating point, but there will be those 
who will insist on an additional
varchar field.

True, this doesn't accomodate the additional parameters that were 
passed to property, above, I have to
think about that...

Brian O.


On Wednesday, February 19, 2003, at 03:24 PM, Aaron J Mackey wrote:

>
> 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
>
>
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