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Manual Reference Pages  -  BIO::TOOLS::PROTPARAM (3)

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NAME

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

CONTENTS

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

    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



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perl v5.20.3 BIO::TOOLS::PROTPARAM (3) 2016-04-05

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