pICalculator 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://www.hgmp.mrc.ac.uk/Software/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.

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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ 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 _.

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