Christopher Fields > BioPerl-1.6.922 > Bio::Variation::AAChange



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Module Version: 1.006922   Source   Latest Release: BioPerl-1.6.924


Bio::Variation::AAChange - Sequence change class for polypeptides


   $aamut = Bio::Variation::AAChange->new
       ('-start'         => $start,
        '-end'           => $end,
        '-length'        => $len,
        '-proof'         => $proof,
        '-isMutation'    => 1,
        '-mut_number'    => $mut_number

   my $a1 = Bio::Variation::Allele->new;
   $a1->seq($ori) if $ori;
   my $a2 = Bio::Variation::Allele->new;
   $a2->seq($mut) if $mut;

   print  "\n";

   # add it to a SeqDiff container object

   # and create links to and from RNA level variant objects


The instantiable class Bio::Variation::RNAChange describes basic sequence changes at polypeptide level. It uses methods defined in superclass Bio::Variation::VariantI, see Bio::Variation::VariantI for details.

If the variation described by a AAChange object has a known Bio::Variation::RNAAChange object, create the link with method AAChange(). See Bio::Variation::AAChange for more information.


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Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

AUTHOR - Heikki Lehvaslaiho ^

Email: heikki-at-bioperl-dot-org


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


 Title   : RNAChange
 Usage   : $mutobj = $self->RNAChange;
         : $mutobj = $self->RNAChange($objref);
 Function: Returns or sets the link-reference to a mutation/change object.
           If there is no link, it will return undef
 Returns : an obj_ref or undef


 Title   : label
 Usage   : $obj->label();

            Sets and returns mutation event label(s).  If value is not
            set, or no argument is given returns false.  Each
            instantiable subclass of L<Bio::Variation::VariantI> needs
            to implement this method. Valid values are listed in
            'Mutation event controlled vocabulary' in

 Example : 
 Returns : string
 Args    : string


 Title   : similarity_score
 Usage   : $self->similarity_score
 Function: Measure for evolutionary conservativeness
           of single amino substitutions. Uses BLOSUM62.
           Negative numbers are noncoservative changes.
 Returns : integer, undef if not single amino acid change


 Title   : trivname
 Usage   : $self->trivname

           Given a Bio::Variation::AAChange object with linked
           Bio::Variation::RNAChange and Bio::Variation::DNAMutation
           objects, this subroutine creates a string corresponding to
           the 'trivial name' of the mutation. Trivial name is
           specified in Antonorakis & MDI Nomenclature Working Group:
           Human Mutation 11:1-3, 1998.

 Returns : string
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