| Bio::Tools::pICalculator(3pm) | User Contributed Perl Documentation | Bio::Tools::pICalculator(3pm) |
Bio::Tools::pICalculator - calculate the isoelectric point of a protein
Calculates the isoelectric point of a protein, the pH at which there is no overall charge on the protein. Calculates the charge on a protein at a given pH. Can use built-in sets of pK values or custom pK sets.
use Bio::Tools::pICalculator;
use Bio::SeqIO;
my $in = Bio::SeqIO->new( -fh => \*STDIN ,
-format => 'Fasta' );
my $calc = Bio::Tools::pICalculator->new(-places => 2,
-pKset => 'EMBOSS');
while ( my $seq = $in->next_seq ) {
$calc->seq($seq);
my $iep = $calc->iep;
print sprintf( "%s\t%s\t%.2f\n",
$seq->id,
$iep,
$calc->charge_at_pH($iep) );
for( my $i = 0; $i <= 14; $i += 0.5 ){
print sprintf( "pH = %.2f\tCharge = %.2f\n",
$i,
$calc->charge_at_pH($i) );
}
}
http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf http://emboss.sourceforge.net/apps/cvs/emboss/apps/iep.html http://us.expasy.org/tools/pi_tool.html
There are various sources for the pK values of the amino acids. The set of pK values chosen will affect the pI reported.
The charge state of each residue is assumed to be independent of the others. Protein modifications (such as a phosphate group) that have a charge are ignored.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
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Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
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Mark Southern (mark_southern@merck.com). From an algorithm by David Tabb found at http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf. Modification for Bioperl, additional documentation by Brian Osborne.
Copyright (c) 2002, Merck & Co. Inc. All Rights Reserved. This module is free software. It may be used, redistributed and/or modified under the terms of the Perl Artistic License (see http://www.perl.com/perl/misc/Artistic.html)
The rest of the documentation details each of the object methods. Private methods are usually preceded by a _.
Title : new
Usage : Bio::Tools::pICalculator->new
Function: Instantiates the Bio::Tools::pICalculator object
Example : $calc = Bio::Tools::pICalculator->new( -pKset => \%pKvalues,
# a Bio::Seq object
-seq => $seq,
-places => 2 );
or:
$calc = Bio::Tools::pICalculator->new( -pKset => 'string',
# a Bio::Seq object
-seq => $seq,
-places => 1 );
Constructs a new pICalculator. Arguments are a flattened hash.
Valid, optional keys are:
pKset - A reference to a hash with key value pairs for the
pK values of the charged amino acids. Required keys
are:
N_term C_term K R H D E C Y
pKset - A string ( 'DTASelect' or 'EMBOSS' ) that will
specify an internal set of pK values to be used. The
default is 'EMBOSS'
seq - A Bio::Seq sequence object to analyze
places - The number of decimal places to use in the
isoelectric point calculation. The default is 2.
Returns : The description
Args : The description or none
Title : seq
Usage : $calc->seq($seqobj)
Function: Sets or returns the Bio::Seq used in the calculation
Example : $seqobj = Bio::Seq->new(-seq=>"gghhhmmm",-id=>"GHM");
$calc = Bio::Tools::pICalculator->new;
$calc->seq($seqobj);
Returns : Bio::Seq object
Args : Bio::Seq object or none
Title : pKset
Usage : $pkSet = $calc->pKSet(\%pKSet)
Function: Sets or returns the hash of pK values used in the calculation
Example : $calc->pKset('emboss')
Returns : reference to pKset hash
Args : The reference to a pKset hash, a string, or none. Examples:
pKset - A reference to a hash with key value pairs for the
pK values of the charged amino acids. Required keys
are:
N_term C_term K R H D E C Y
pKset - A valid string ( 'DTASelect' or 'EMBOSS' ) that will
specify an internal set of pK values to be used. The
default is 'EMBOSS'
Title : iep
Usage : $calc->iep
Function: Returns the isoelectric point
Example : $calc = Bio::Tools::pICalculator->new(-places => 2);
$calc->seq($seqobj);
$iep = $calc->iep;
Returns : The isoelectric point of the sequence in the Bio::Seq object
Args : None
Title : charge_at_pH
Usage : $charge = $calc->charge_at_pH($pH)
Function: Sets or gets the description of the sequence
Example : $calc = Bio::Tools::pICalculator->new(-places => 2);
$calc->seq($seqobj);
$charge = $calc->charge_at_ph("7");
Returns : The predicted charge at the given pH
Args : pH
| 2018-10-27 | perl v5.26.2 |