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Inputting info
01-17-2012
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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)