Modware

Protein_info

   Modware::Protein_info - Results of many calculations based on protein sequence.

  # SEE DESCRIPTION FOR AUTOLOADED METHODS WHICH DO NOT APPEAR IN THIS DOC!!!!!!!!!

  # THIS CLASS SHOULD ONLY BE USED THROUGH THE FEATURE OBJECT

  # USE CASE: ACCESS MOLECULAR WEIGHT AND N-TERMINAL SEQ FOR A FEATURE

      my $feature = new Modware::Feature( -primary_id => 'DDB0191090' );

      print $feature->protein_info->molecular_weight(),"\n";
      print $feature->protein_info->n_term_seq(),"\n";

   Since this class calculates protein info on a feature in the database, a feature_id is a
   required argument to new.  Creating a new object will pull all of the stored protein_info
   from the database into the object.   If you wish to update the protein_info based on a new 
   sequence, you have to change the sequence through the seq

   Since this class uses the Class::Accessor superclass, there are many methods that do no appear
   in the list genereated by pdoc.  Each of the amino acid counts can be accessed by one of the following:

   ala arg asn asp cys 
   gln glu gly his ile 
   leu lys met phe pro 
   ser thr trp tyr val

   Other mehtods available are:

   molecular_weight  : get/set Molecular weight of protein sequence
   protein_length    : get/set length of the protein
   n_term_seq        : get/set n-terminal sequence of the protein seq
   c_term_seq        : get/set c-terminal sequence of the protein seq

Methods description

 Title    : calculate 
 Function : when sequence changes, you want protein info on that sequence,
          : not what is in the database, this method recalculates all info based
          : on this new sequence
 Returns  : nothing
 Args     : none

 Title    : new
 Usage    : generally used through the feature object
 Function : creates a new protein info object
 Returns  : Modware::Protein_info object
 Args     : reference to sequenc (required)

 Title    : percent
 Function : calculate percentage of total aa's that particular aa is present in sequence
 Usage    : print "The percent of arginine is ".$prot_info->percent( 'arg' );
 Returns  : percentage
 Args     : 3 letter amino acid code ( arg, cys etc) case insensitive

 Title    : protein_lookup
 Note     : protein_lookup is a hash keyed on 3 letter code accessors.  the values are
          : the one letter codes that show up in the sequence. example:
          : $prot_info->protein_lookup{'ala'} would return 'A'
 Function : gets protein_lookup hash
 Returns  : protein_lookup hash
 Args     : protein_lookup ( optional )

 Title    : sequence
 Function : get/set sequence
 Note     : need to call 'calculate' after sequence has been changed
 Returns  : protein sequence
 Args     : protein sequence ( optional )

Methods code

   my ($self, @args) = @_;

   $seqobj     = Bio::PrimarySeq->new(  -seq => $self->sequence, -alphabet => 'protein'  );

   $seq_stats  =  Bio::Tools::SeqStats->new(-seq=>$seqobj);

   $count_ref = $seq_stats->count_monomers();  # eg for DNA sequence  

   my @amino_acids = qw(ala arg asn asp cys gln glu gly his ile leu lys met phe pro ser thr trp tyr val);  

   foreach my $aa ( @amino_acids ) {
      $count_ref->{ $protein_lookup{ $aa } } = 0 if !$count_ref->{ $protein_lookup{ $aa } };
      my $accessor_name = lc($aa);
      #print $count_ref->{ $protein_lookup{ $aa } }."\n";
      $self->$accessor_name( $count_ref->{ $protein_lookup{ $aa } } );
   }

#   my $iep =   $analysis->wait_for ( { 'sequencea_direct_data' => $display_seq } ) ->result;
#   my @tmp = ($iep =~ /Isoelectric Point = ([\d\.]+)/);
#   $iep = $tmp[0];

   $self->molecular_weight( $seq_stats->get_mol_wt()->[0] );
   $self->protein_length( $seqobj->length );
   $self->n_term_seq( $seqobj->length >= 7 ? $seqobj->subseq(1,7)  : $seqobj->seq );
   $self->c_term_seq( $seqobj->length >= 7 ? $seqobj->subseq($seqobj->length - 6,$seqobj->length): $seqobj->seq );

   my ($class, $seqref) = @_;

   my $self = {};
   bless $self, $class;

   my $seq = $$seqref;
      
   $seq =~ s/\*//g;
   $self->sequence( $seq );

   $self->calculate();
   return $self;

   my ( $self, $aa ) = @_;

   if ( !$aa || !$self->protein_lookup->{$aa} ) { 
      $self->throw(" need to pass in valid 3 letter amino acid code to calculate percent ");
   }
   $aa = lc($aa);
   return sprintf("%.1f", $self->$aa/$self->protein_length*100);

   return\% protein_lookup;

   my ($self, $obj) = @_;
   if($obj) {
      $self->{sequence} = $obj;
   }
   return $self->{sequence};

General documentation

   Eric Just e-just@northwestern.edu

   The rest of the documentation details each of the object
   methods. Internal methods are usually preceded with a _

Copyright © 2006, Northwestern University All rights reserved.