Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Variation::DNAMutation - DNA level mutation class


           $dnamut = Bio::Variation::DNAMutation->new
               ('-start'         => $start,
                '-end'           => $end,
                '-length'        => $len,
                '-upStreamSeq'   => $upflank,
                '-dnStreamSeq'   => $dnflank,
                '-proof'         => $proof,
                '-isMutation'    => 1,
                '-mut_number'    => $mut_number
           $a1 = Bio::Variation::Allele->new;
           my $a2 = Bio::Variation::Allele->new;

           print "Restriction changes are ", $dnamut->restriction_changes, "\n";

           # add it to a SeqDiff container object


       The instantiable class Bio::Variation::DNAMutation describes basic sequence changes in
       genomic DNA level. It uses methods defined in superclass Bio::Variation::VariantI. See
       Bio::Variation::VariantI for details.

       If the variation described by a DNAMutation object is transcibed, link the corresponding
       Bio::Variation::RNAChange object to it using method RNAChange(). See
       Bio::Variation::RNAChange for more information.


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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   : CpG
        Usage   : $obj->CpG()
        Function: sets and returns boolean values for variation
                  hitting a CpG site.  Unset value return -1.
        Example : $obj->CpG()
        Returns : boolean
        Args    : optional true of false value

        Title   : RNAChange
        Usage   : $mutobj = $obj->RNAChange;
                : $mutobj = $obj->RNAChange($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   : sysname
        Usage   : $self->sysname

                  This subroutine creates a string corresponding to the
                  'systematic name' of the mutation. Systematic name is
                  specified in Antonorakis & MDI Nomenclature Working Group:
                  Human Mutation 11:1-3, 1998.

        Returns : string