Bio::Variation::RNAChange - Sequence change class for RNA level $rnachange = Bio::Variation::RNAChange->new ('-start' => $start, '-end' => $end, '-length' => $len, '-codon_pos' => $cp, '-upStreamSeq' => $upflank, '-dnStreamSeq' => $dnflank, '-proof' => $proof, '-isMutation' => 1, '-mut_number' => $mut_number ); $a1 = Bio::Variation::Allele->new; $a1->seq('a'); $rnachange->allele_ori($a1); my $a2 = Bio::Variation::Allele->new; $a2->seq('t'); $rnachange->add_Allele($a2); $rnachange->allele_mut($a2); print "The codon change is ", $rnachange->codon_ori, ">", $rnachange->codon_mut, "\n"; # add it to a SeqDiff container object $seqdiff->add_Variant($rnachange); # and create links to and from DNA level mutation objects $rnachange->DNAMutation($dnamut); $dnamut->RNAChange($rnachange); The instantiable class Bio::Variation::DNAMutation describes basic sequence changes at RNA molecule level. It uses methods defined in superclass Bio::Variation::VariantI. See Bio::Variation::VariantI for details. You are normally expected to create a corresponding Bio::Variation::DNAMutation object even if mutation is defined at RNA level. The numbering follows then cDNA numbering. Link the DNAMutation object to the RNAChange object using the method DNAMutation(). If the variation described by a RNAChange object is translated, link the corresponding Bio::Variation::AAChange object to it using method AAChange(). See Bio::Variation::DNAMutation and Bio::Variation::AAChange for more information.

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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/ 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 _

codon_ori
Title : codon_ori Usage : $obj->codon_ori(); Function: Sets and returns codon_ori triplet. If value is not set, creates the codon triplet from the codon position and flanking sequences. The string has to be three characters long. The character content is not checked. Example : Returns : string Args : string

codon_mut
Title : codon_mut Usage : $obj->codon_mut(); Function: Sets and returns codon_mut triplet. If value is not set, creates the codon triplet from the codon position and flanking sequences. Return undef for other than point mutations. Example : Returns : string Args : string

codon_pos
Title : codon_pos Usage : $obj->codon_pos(); Function: Sets and returns the position of the mutation start in the codon. If value is not set, returns false. Example : Returns : 1,2,3 Args : none if get, the new value if set

codon_table
Title : codon_table Usage : $obj->codon_table(); Function: Sets and returns the codon table id of the RNA If value is not set, returns 1, 'universal' code, as the default. Example : Returns : integer Args : none if get, the new value if set

DNAMutation
Title : DNAMutation Usage : $mutobj = $obj->DNAMutation; : $mutobj = $obj->DNAMutation($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

AAChange
Title : AAChange Usage : $mutobj = $obj->AAChange; : $mutobj = $obj->AAChange($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

exons_modified
Title : exons_modified Usage : $modified = $obj->exons_modified; : $modified = $obj->exons_modified(1); Function: Returns or sets information (example: a simple boolean flag) about the modification of exons as a result of a mutation.

region
Title : region Usage : $obj->region(); Function: Sets and returns the name of the sequence region type or protein domain at this location. If value is not set, returns false. Example : Returns : string Args : string

cds_end
Title : cds_end Usage : $cds_end = $obj->get_cds_end(); Function: Sets or returns the cds_end from the beginning of the DNA sequence to the coordinate start used to describe variants. Should be the location of the last nucleotide of the terminator codon of the gene. Example : Returns : value of cds_end, a scalar Args :

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

_change_codon_pos
Title : _change_codon_pos Usage : $newCodonPos = _change_codon_pos($myCodonPos, 5) Function: Keeps track of the codon position in a changeing sequence Returns : codon_pos = integer 1, 2 or 3 Args : valid codon position signed integer offset to a new location in sequence