Bio::Tools::Protparam3pm
Submit to and parse output from protparam ;
Usage
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);"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";}
Overview
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.
Releases
5 releases since Debian 6.0 (Squeeze); the text changed 4 times.