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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 : ", $seq->display_id,"\n",
         "Amino acid number : ",$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