Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

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

SYNOPSIS

           $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;
           $a1->seq('a');
           $dnamut->allele_ori($a1);
           my $a2 = Bio::Variation::Allele->new;
           $a2->seq('t');
           $dnamut->add_Allele($a2);

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

           # add it to a SeqDiff container object
           $seqdiff->add_Variant($dnamut);

DESCRIPTION

       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.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing lists  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       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:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho

       Email:  heikki-at-bioperl-dot-org

APPENDIX

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

   CpG
        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

   RNAChange
        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

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

                   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
                   http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.

        Example :
        Returns : string
        Args    : string

   sysname
        Title   : sysname
        Usage   : $self->sysname
        Function:

                  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