[Bioperl-l] isoelectric point

[Heikki Lehvaslaiho]

Harald.Weber@bioperl.org wrote:
> 
> Hi, I'm  a Newbie !
> 
> There's a Bioperl-routine to calculate the
> molecular weight of a protein.
> 
> Is there also something to calculate the isoelectric point (pI) ?

Harald,

Aaron C-code might find itself in bioperl some day, but as an exercise
I wrote a script which uses a locally installed EMBOSS iep program.

Neat and short, isn't it?

	-Heikki

-------------ipoint.pl------------------

use Bio::Factory::EMBOSS;
use Bio::PrimarySeq;
use strict;

# assuming you have a bioperl sequence object
# you want to analyze, we create one in memory

my $seq = new Bio::PrimarySeq (
                                -id => 'testprotein',
                                -alphabet => 'protein',
                                -seq => 'gcklimps'
                                );

my $factory = new Bio::Factory::EMBOSS();
my $ipoint = $factory->program('iep');

my %input = (-sequencea => $seq,
             -outfile => 'stdout'
             );

my $out = $ipoint->run(\%input);
my ($iep) = $out =~ /Isoelectric Point = ([\d\.]+)/;
print "$iep\n";