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)