NAME¶

Bio::Tools::Protparam - submit to and parse output from protparam ;

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";
}

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

  Title    : new
  Usage    : $pp = Protparam->new(seq=>$seq->seq);
  Function : Creates a new Protparam object
  Returns  : A Protparam object
  Args     : A sequence

  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

  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

  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

  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

  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

  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

  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

  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

  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

  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

  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

  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

  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

  Title    : stability
  Usage    : $pp->stability()
  Function : Calculates whether the sequence is stable or unstable
  Returns  : 'stable' or 'unstable'
  Args     : none

  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

  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

  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