Bio::Tools::Protparam(3pm) User Contributed Perl Documentation Bio::Tools::Protparam(3pm)
NAME
Bio::Tools::Protparam - submit to and parse output from protparam ;
SYNOPSIS
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 $pp = Protparam->new(seq=>$seq->seq);
print
"ID : ", $seq->display_id,"
",
"Amino acid number : ",$pp->amino_acid_number(),"
",
"Number of negative amino acids : ",$pp->num_neg(),"
",
"Number of positive amino acids : ",$pp->num_pos(),"
",
"Molecular weight : ",$pp->molecular_weight(),"
",
"Theoretical pI : ",$pp->theoretical_pI(),"
",
"Total number of atoms : ", $pp->total_atoms(),"
",
"Number of carbon atoms : ",$pp->num_carbon(),"
",
"Number of hydrogen atoms : ",$pp->num_hydrogen(),"
",
"Number of nitrogen atoms : ",$pp->num_nitro(),"
",
"Number of oxygen atoms : ",$pp->num_oxygen(),"
",
"Number of sulphur atoms : ",$pp->num_sulphur(),"
",
"Half life : ", $pp->half_life(),"
",
"Instability Index : ", $pp->instability_index(),"
",
"Stability class : ", $pp->stability(),"
",
"Aliphatic_index : ",$pp->aliphatic_index(),"
",
"Gravy : ", $pp->gravy(),"
",
"Composition of A : ", $pp->AA_comp('A'),"
",
"Composition of R : ", $pp->AA_comp('R'),"
",
"Composition of N : ", $pp->AA_comp('N'),"
",
"Composition of D : ", $pp->AA_comp('D'),"
",
"Composition of C : ", $pp->AA_comp('C'),"
",
"Composition of Q : ", $pp->AA_comp('Q'),"
",
"Composition of E : ", $pp->AA_comp('E'),"
",
"Composition of G : ", $pp->AA_comp('G'),"
",
"Composition of H : ", $pp->AA_comp('H'),"
",
"Composition of I : ", $pp->AA_comp('I'),"
",
"Composition of L : ", $pp->AA_comp('L'),"
",
"Composition of K : ", $pp->AA_comp('K'),"
",
"Composition of M : ", $pp->AA_comp('M'),"
",
"Composition of F : ", $pp->AA_comp('F'),"
",
"Composition of P : ", $pp->AA_comp('P'),"
",
"Composition of S : ", $pp->AA_comp('S'),"
",
"Composition of T : ", $pp->AA_comp('T'),"
",
"Composition of W : ", $pp->AA_comp('W'),"
",
"Composition of Y : ", $pp->AA_comp('Y'),"
",
"Composition of V : ", $pp->AA_comp('V'),"
",
"Composition of B : ", $pp->AA_comp('B'),"
",
"Composition of Z : ", $pp->AA_comp('Z'),"
",
"Composition of X : ", $pp->AA_comp('X'),"
";
}
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.
AUTHOR
Richard Dobson, r.j.dobson at qmul dot ac dot uk
new
Title : new
Usage : $pp = Protparam->new(seq=>$seq->seq);
Function : Creates a new Protparam object
Returns : A Protparam object
Args : A sequence
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
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
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
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
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
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
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
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
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
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
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
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
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
stability
Title : stability
Usage : $pp->stability()
Function : Calculates whether the sequence is stable or unstable
Returns : 'stable' or 'unstable'
Args : none
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
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
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
perl v5.14.2 2012-03-02 Bio::Tools::Protparam(3pm)