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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Protparam 3pm"
.TH Bio::Tools::Protparam 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tools::Protparam \- submit to and parse output from protparam ;
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  use Bio::DB::GenBank;
\&  use Bio::Tools::Protparam;
\&
\&  my $gb = new Bio::DB::GenBank(\-retrievaltype => \*(Aqtempfile\*(Aq , 
\&                                \-format => \*(AqFasta\*(Aq);
\&  my @ids=qw(O14521 O43709 O43826);
\&  my $seqio = $gb\->get_Stream_by_acc(\e@ids );
\&
\&  while( my $seq =  $seqio\->next_seq ) {
\&
\&        my $pp = Bio::Tools::Protparam\->new(seq=>$seq\->seq);
\&
\&        print
\&        "ID : ", $seq\->display_id,"\en",
\&        "Amino acid number : ",$pp\->amino_acid_number(),"\en",
\&        "Number of negative amino acids : ",$pp\->num_neg(),"\en",
\&        "Number of positive amino acids : ",$pp\->num_pos(),"\en",
\&        "Molecular weight : ",$pp\->molecular_weight(),"\en",
\&        "Theoretical pI : ",$pp\->theoretical_pI(),"\en",
\&        "Total number of atoms : ", $pp\->total_atoms(),"\en",
\&        "Number of carbon atoms : ",$pp\->num_carbon(),"\en",
\&        "Number of hydrogen atoms : ",$pp\->num_hydrogen(),"\en",
\&        "Number of nitrogen atoms : ",$pp\->num_nitro(),"\en",
\&        "Number of oxygen atoms : ",$pp\->num_oxygen(),"\en",
\&        "Number of sulphur atoms : ",$pp\->num_sulphur(),"\en",
\&        "Half life : ", $pp\->half_life(),"\en",
\&        "Instability Index : ", $pp\->instability_index(),"\en",
\&        "Stability class : ", $pp\->stability(),"\en",
\&        "Aliphatic_index : ",$pp\->aliphatic_index(),"\en",
\&        "Gravy : ", $pp\->gravy(),"\en",
\&        "Composition of A : ", $pp\->AA_comp(\*(AqA\*(Aq),"\en",
\&        "Composition of R : ", $pp\->AA_comp(\*(AqR\*(Aq),"\en",
\&        "Composition of N : ", $pp\->AA_comp(\*(AqN\*(Aq),"\en",
\&        "Composition of D : ", $pp\->AA_comp(\*(AqD\*(Aq),"\en",
\&        "Composition of C : ", $pp\->AA_comp(\*(AqC\*(Aq),"\en",
\&        "Composition of Q : ", $pp\->AA_comp(\*(AqQ\*(Aq),"\en",
\&        "Composition of E : ", $pp\->AA_comp(\*(AqE\*(Aq),"\en",
\&        "Composition of G : ", $pp\->AA_comp(\*(AqG\*(Aq),"\en",
\&        "Composition of H : ", $pp\->AA_comp(\*(AqH\*(Aq),"\en",
\&        "Composition of I : ", $pp\->AA_comp(\*(AqI\*(Aq),"\en",
\&        "Composition of L : ", $pp\->AA_comp(\*(AqL\*(Aq),"\en",
\&        "Composition of K : ", $pp\->AA_comp(\*(AqK\*(Aq),"\en",
\&        "Composition of M : ", $pp\->AA_comp(\*(AqM\*(Aq),"\en",
\&        "Composition of F : ", $pp\->AA_comp(\*(AqF\*(Aq),"\en",
\&        "Composition of P : ", $pp\->AA_comp(\*(AqP\*(Aq),"\en",
\&        "Composition of S : ", $pp\->AA_comp(\*(AqS\*(Aq),"\en",
\&        "Composition of T : ", $pp\->AA_comp(\*(AqT\*(Aq),"\en",
\&        "Composition of W : ", $pp\->AA_comp(\*(AqW\*(Aq),"\en",
\&        "Composition of Y : ", $pp\->AA_comp(\*(AqY\*(Aq),"\en",
\&        "Composition of V : ", $pp\->AA_comp(\*(AqV\*(Aq),"\en",
\&        "Composition of B : ", $pp\->AA_comp(\*(AqB\*(Aq),"\en",
\&        "Composition of Z : ", $pp\->AA_comp(\*(AqZ\*(Aq),"\en",
\&        "Composition of X : ", $pp\->AA_comp(\*(AqX\*(Aq),"\en";
\&}
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "AUTHOR"
.IX Header "AUTHOR"
Richard Dobson, r.j.dobson at qmul dot ac dot uk
.SS "new"
.IX Subsection "new"
.Vb 5
\&  Title    : new
\&  Usage    : $pp = Protparam\->new(seq=>$seq\->seq);
\&  Function : Creates a new Protparam object
\&  Returns  : A Protparam object
\&  Args     : A sequence
.Ve
.SS "num_neg"
.IX Subsection "num_neg"
.Vb 5
\&  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
.Ve
.SS "num_pos"
.IX Subsection "num_pos"
.Vb 5
\&  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
.Ve
.SS "amino_acid_number"
.IX Subsection "amino_acid_number"
.Vb 5
\&  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
.Ve
.SS "total_atoms"
.IX Subsection "total_atoms"
.Vb 5
\&  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
.Ve
.SS "molecular_weight"
.IX Subsection "molecular_weight"
.Vb 5
\&  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
.Ve
.SS "theoretical_pI"
.IX Subsection "theoretical_pI"
.Vb 5
\&  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
.Ve
.SS "num_carbon"
.IX Subsection "num_carbon"
.Vb 5
\&  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
.Ve
.SS "num_hydrogen"
.IX Subsection "num_hydrogen"
.Vb 5
\&  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
.Ve
.SS "num_nitro"
.IX Subsection "num_nitro"
.Vb 5
\&  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
.Ve
.SS "num_oxygen"
.IX Subsection "num_oxygen"
.Vb 5
\&  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
.Ve
.SS "num_sulphur"
.IX Subsection "num_sulphur"
.Vb 5
\&  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
.Ve
.SS "half_life"
.IX Subsection "half_life"
.Vb 5
\&  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
.Ve
.SS "instability_index"
.IX Subsection "instability_index"
.Vb 5
\&  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
.Ve
.SS "stability"
.IX Subsection "stability"
.Vb 5
\&  Title    : stability
\&  Usage    : $pp\->stability()
\&  Function : Calculates whether the sequence is stable or unstable
\&  Returns  : \*(Aqstable\*(Aq or \*(Aqunstable\*(Aq
\&  Args     : none
.Ve
.SS "aliphatic_index"
.IX Subsection "aliphatic_index"
.Vb 5
\&  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
.Ve
.SS "gravy"
.IX Subsection "gravy"
.Vb 5
\&  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
.Ve
.SS "AA_comp"
.IX Subsection "AA_comp"
.Vb 5
\&  Title    : AA_comp
\&  Usage    : $pp\->AA_comp(\*(AqP\*(Aq)
\&  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
.Ve