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) );
     }
  }

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:

  https://github.com/bioperl/bioperl-live/issues

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