#
# BioPerl module for Bio::Tools::Protparam
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Richard Dobson, r.j.dobson at qmul dot ac dot uk
#
# Copyright Richard Dobson
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Protparam - submit to and parse output from protparam ;
=head1 SYNOPSIS
use Bio::DB::GenBank;
use Bio::Tools::Protparam;
my $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile' ,
-format => 'Fasta');
my @ids=qw(O14521 O43709 O43826);
my $seqio = $gb->get_Stream_by_acc(\@ids );
while( my $seq = $seqio->next_seq ) {
my $pp = Bio::Tools::Protparam->new(seq=>$seq->seq);
print
"ID : ", $seq->display_id,"\n",
"Amino acid number : ",$pp->amino_acid_number(),"\n",
"Number of negative amino acids : ",$pp->num_neg(),"\n",
"Number of positive amino acids : ",$pp->num_pos(),"\n",
"Molecular weight : ",$pp->molecular_weight(),"\n",
"Theoretical pI : ",$pp->theoretical_pI(),"\n",
"Total number of atoms : ", $pp->total_atoms(),"\n",
"Number of carbon atoms : ",$pp->num_carbon(),"\n",
"Number of hydrogen atoms : ",$pp->num_hydrogen(),"\n",
"Number of nitrogen atoms : ",$pp->num_nitro(),"\n",
"Number of oxygen atoms : ",$pp->num_oxygen(),"\n",
"Number of sulphur atoms : ",$pp->num_sulphur(),"\n",
"Half life : ", $pp->half_life(),"\n",
"Instability Index : ", $pp->instability_index(),"\n",
"Stability class : ", $pp->stability(),"\n",
"Aliphatic_index : ",$pp->aliphatic_index(),"\n",
"Gravy : ", $pp->gravy(),"\n",
"Composition of A : ", $pp->AA_comp('A'),"\n",
"Composition of R : ", $pp->AA_comp('R'),"\n",
"Composition of N : ", $pp->AA_comp('N'),"\n",
"Composition of D : ", $pp->AA_comp('D'),"\n",
"Composition of C : ", $pp->AA_comp('C'),"\n",
"Composition of Q : ", $pp->AA_comp('Q'),"\n",
"Composition of E : ", $pp->AA_comp('E'),"\n",
"Composition of G : ", $pp->AA_comp('G'),"\n",
"Composition of H : ", $pp->AA_comp('H'),"\n",
"Composition of I : ", $pp->AA_comp('I'),"\n",
"Composition of L : ", $pp->AA_comp('L'),"\n",
"Composition of K : ", $pp->AA_comp('K'),"\n",
"Composition of M : ", $pp->AA_comp('M'),"\n",
"Composition of F : ", $pp->AA_comp('F'),"\n",
"Composition of P : ", $pp->AA_comp('P'),"\n",
"Composition of S : ", $pp->AA_comp('S'),"\n",
"Composition of T : ", $pp->AA_comp('T'),"\n",
"Composition of W : ", $pp->AA_comp('W'),"\n",
"Composition of Y : ", $pp->AA_comp('Y'),"\n",
"Composition of V : ", $pp->AA_comp('V'),"\n",
"Composition of B : ", $pp->AA_comp('B'),"\n",
"Composition of Z : ", $pp->AA_comp('Z'),"\n",
"Composition of X : ", $pp->AA_comp('X'),"\n";
}
=head1 DESCRIPTION
This module takes an amino acid sequence and submits it to the
Protparam program at www.expasy.org/cgi-bin/protparam. Many
properties of the submitted sequence are returned.
=head1 AUTHOR
Richard Dobson, r.j.dobson at qmul dot ac dot uk
=cut
# Let the code begin...
package Bio::Tools::Protparam;
use strict;
use base qw(Bio::Root::Root);
use LWP 5.64;
=head2 new
Title : new
Usage : $pp = Protparam->new(seq=>$seq->seq);
Function : Creates a new Protparam object
Returns : A Protparam object
Args : A sequence
=cut
sub new {
my ($class,@args) = @_;
@args=('-url'=>'http://web.expasy.org/cgi-bin/protparam/protparam','-form'=>'sequence',@args);
my $self=$class->SUPER::new(@args);
my ($url,$seq,$form)=$self->_rearrange([qw(URL SEQ FORM)],@args);
my $browser = LWP::UserAgent->new;
my $response;
#send request to PROTPARAM @ Expasy
$response = $browser->post($url,
[
$form => $seq
],
'User-Agent' => 'Mozilla/4.76 [en] (Win2000; U)',
);
#Check if successful
$self->throw("$url error: ".$response->status_line) unless $response->is_success;
$self->throw("Bad content type at $url ".$response->content_type) unless $response->content_type eq 'text/html';
my $protParamOutput=$response->decoded_content;
$self->{'output'}=$protParamOutput;
return bless $self,$class;
}
=head2 num_neg
Title : num_neg
Usage : $pp->num_neg()
Function : Retrieves the number of negative amino acids in a sequence
Returns : Returns the number of negative amino acids in a sequence
Args : none
=cut
sub num_neg{
my $self=shift;
($self->{'negAA'})=$self->{'output'}=~/<B>Total number of negatively charged residues.*?<\/B>\s*(\d*)/;
return $self->{'negAA'};
}
=head2 num_pos
Title : num_pos
Usage : $pp->num_pos()
Function : Retrieves the number of positive amino acids in a sequence
Returns : Returns the number of positive amino acids in a sequence
Args : none
=cut
sub num_pos{
my $self=shift;
($self->{'posAA'})=$self->{'output'}=~/<B>Total number of positively charged residues.*?<\/B>\s*(\d*)/;
return $self->{'posAA'};
}
=head2 amino_acid_number
Title : amino_acid_number
Usage : $pp->amino_acid_number()
Function : Retrieves the number of amino acids within a sequence
Returns : Returns the number of amino acids within a sequence
Args : none
=cut
sub amino_acid_number{
my $self=shift;
($self->{'numAA'})=$self->{'output'}=~/<B>Number of amino acids:<\/B> (\d+)/;
return $self->{'numAA'};
}
=head2 total_atoms
Title : total_atoms
Usage : $pp->total_atoms()
Function : Retrieves the total number of atoms within a sequence
Returns : Returns the total number of atoms within a sequence
Args : none
=cut
sub total_atoms{
my $self=shift;
$self->{'total_atoms'}=$self->{'output'}=~/<B>Total number of atoms:<\/B>\s*(\d*)/;
return $self->{'total_atoms'};
}
=head2 molecular_weight
Title : molecular_weight
Usage : $pp->molecular_weight()
Function : Retrieves the molecular weight of a sequence
Returns : Returns the molecular weight of a sequence
Args : none
=cut
sub molecular_weight{
my $self=shift;
($self->{'MolWt'})=$self->{'output'}=~/<B>Molecular weight:<\/B> (\d*\.{0,1}\d*)/;
return $self->{'MolWt'};
}
=head2 theoretical_pI
Title : theoretical_pI
Usage : $pp->theoretical_pI()
Function : Retrieve the theoretical pI for a sequence
Returns : Return the theoretical pI for a sequence
Args : none
=cut
sub theoretical_pI{
my $self=shift;
($self->{'TpI'})=$self->{'output'}=~/<B>Theoretical pI:<\/B> (-{0,1}\d*\.{0,1}\d*)/;
return $self->{'TpI'};
}
=head2 num_carbon
Title : num_carbon
Usage : $pp->num_carbon()
Function : Retrieves the number of carbon atoms in a sequence
Returns : Returns the number of carbon atoms in a sequence
Args : none
=cut
sub num_carbon{
my $self=shift;
($self->{'car'}) = $self->{'output'}=~/Carbon\s+C\s+(\d+)/;
return $self->{'car'};
}
=head2 num_hydrogen
Title : num_hydrogen
Usage : $pp->num_hydrogen
Function : Retrieves the number of hydrogen atoms in a sequence
Returns : Returns the number of hydrogen atoms in a sequence
Args : none
=cut
sub num_hydrogen{
my $self=shift;
($self->{'hyd'}) = $self->{'output'}=~/Hydrogen\s+H\s+(\d+)/;
return $self->{'hyd'}
}
=head2 num_nitro
Title : num_nitro
Usage : $pp->num_nitro
Function : Retrieves the number of nitrogen atoms in a sequence
Returns : Returns the number of nitrogen atoms in a sequence
Args : none
=cut
sub num_nitro{
my $self=shift;
($self->{'nitro'}) = $self->{'output'}=~/Nitrogen\s+N\s+(\d+)/;
return $self->{'nitro'};
}
=head2 num_oxygen
Title : num_oxygen
Usage : $pp->num_oxygen()
Function : Retrieves the number of oxygen atoms in a sequence
Returns : Returns the number of oxygen atoms in a sequence
Args : none
=cut
sub num_oxygen{
my $self=shift;
($self->{'oxy'}) = $self->{'output'}=~/Oxygen\s+O\s+(\d+)/;
return $self->{'oxy'};
}
=head2 num_sulphur
Title : num_sulphur
Usage : $pp->num_sulphur()
Function : Retrieves the number of sulphur atoms in a sequence
Returns : Returns the number of sulphur atoms in a sequence
Args : none
=cut
sub num_sulphur{
my $self=shift;
($self->{'sul'}) = $self->{'output'}=~/Sulfur\s+S\s+(\d+)/;
return $self->{'sul'};
}
=head2 half_life
Title : half_life
Usage : $pp->half_life()
Function : Retrieves the half life of a sequence
Returns : Returns the half life of a sequence
Args : none
=cut
sub half_life{
my $self=shift;
($self->{'half_life'}) = $self->{'output'}=~/The estimated half-life is.*?(-{0,1}\d*\.{0,1}\d*)\s*hours \(mammalian reticulocytes, in vitro\)/;
return $self->{'half_life'};
}
=head2 instability_index
Title : instability_index
Usage : $pp->instability_index()
Function : Retrieves the instability index of a sequence
Returns : Returns the instability index of a sequence
Args : none
=cut
sub instability_index{
my $self=shift;
($self->{'InstabilityIndex'})=$self->{'output'}=~/The instability index \(II\) is computed to be (-{0,1}\d*\.{0,1}\d*)/;
return $self->{'InstabilityIndex'};
}
=head2 stability
Title : stability
Usage : $pp->stability()
Function : Calculates whether the sequence is stable or unstable
Returns : 'stable' or 'unstable'
Args : none
=cut
sub stability{
my $self=shift;
($self->{'Stability'})=$self->{'output'}=~/This classifies the protein as\s(\w+)\./;
return $self->{'Stability'};
}
=head2 aliphatic_index
Title : aliphatic_index
Usage : $pp->aliphatic_index()
Function : Retrieves the aliphatic index of the sequence
Returns : Returns the aliphatic index of the sequence
Args : none
=cut
sub aliphatic_index{
my $self=shift;
($self->{'AliphaticIndex'})=$self->{'output'}=~/<B>Aliphatic index:<\/B>\s*(-{0,1}\d*\.{0,1}\d*)/;
return $self->{'AliphaticIndex'};
}
=head2 gravy
Title : gravy
Usage : $pp->gravy()
Function : Retrieves the grand average of hydropathicity (GRAVY) of a sequence
Returns : Returns the grand average of hydropathicity (GRAVY) of a sequence
Args : none
=cut
sub gravy{
my $self=shift;
($self->{'GRAVY'})=$self->{'output'}=~/<B>Grand average of hydropathicity \(GRAVY\):<\/B>\s*(-{0,1}\d*\.{0,1}\d*)/;
return $self->{'GRAVY'};
}
=head2 AA_comp
Title : AA_comp
Usage : $pp->AA_comp('P')
Function : Retrieves the percentage composition of a given amino acid for a sequence
Returns : Returns the percentage composition of a given amino acid for a sequence
Args : A single letter amino acid code eg A, R, G, P etc
=cut
sub AA_comp{
my $self=shift;
my $aa=shift;
$aa=uc($aa);
my $AA={qw(A Ala R Arg N Asn D Asp C Cys Q Gln E Glu G Gly H His I Ile L Leu K Lys M Met F Phe P Pro S Ser T Thr W Trp Y Tyr V Val B Asx Z Glx X Xaa)};
($self->{$aa})= $self->{'output'}=~/$AA->{$aa} \($aa\)\s+\d+\s+(\d+\.\d+)%/;
return $self->{$aa};
}
1;