Bio::Tools::Protparam(3pm) | User Contributed Perl Documentation | Bio::Tools::Protparam(3pm) |
Bio::Tools::Protparam - submit to and parse output from protparam ;
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"; }
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.
Richard Dobson, r.j.dobson at qmul dot ac dot uk
Title : new Usage : $pp = Protparam->new(seq=>$seq->seq); Function : Creates a new Protparam object Returns : A Protparam object Args : A sequence
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
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
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
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
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
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
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
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
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
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
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
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
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
Title : stability Usage : $pp->stability() Function : Calculates whether the sequence is stable or unstable Returns : 'stable' or 'unstable' Args : none
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
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
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
2018-10-27 | perl v5.26.2 |