/ 
bioperl-1.5.2_005-RCb
/ Bio::Tools::pICalculator

NAME

Bio::Tools::pICalculator - calculate the isoelectric point of a protein

DESCRIPTION

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.

SYNOPSIS

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) );
   }
}

SEE ALSO

http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf http://emboss.sourceforge.net/apps/cvs/iep.html http://us.expasy.org/tools/pi_tool.html

LIMITATIONS

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.

FEEDBACK

Mailing Lists

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.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Bugs

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:

http://bugzilla.open-bio.org/

AUTHOR

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

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)

APPENDIX

The rest of the documentation details each of the object methods. Private methods are usually preceded by a _.

desc

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

seq

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

pKset

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'

iep

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

charge_at_pH

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