Bio::Variation::DNAMutation(3) 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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Reporting Bugs

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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