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; $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); The instantiable class Bio::Variation::DNAMutation describes basic sequence changes in genomic DNA level. It uses methods defined in superclass the Bio::Variation::VariantI manpage. If the variation described by a DNAMutation object is transcibed, link the corresponding the Bio::Variation::RNAChange manpage object to it using method RNAChange().

Mailing Lists
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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://bio.perl.org/bioperl-bugs/ Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom 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