Bio::Variation::DNAMutation(3)

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
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  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
 email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

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.
           http://www.interscience.wiley.com/jpages/1059-7794/nomenclature.html
 Returns : string