Bio::Variation::AAChange - Sequence change class for polypeptides $aamut = Bio::Variation::AAChange->new ('-start' => $start, '-end' => $end, '-length' => $len, '-proof' => $proof, '-isMutation' => 1, '-mut_number' => $mut_number ); my $a1 = Bio::Variation::Allele->new; $a1->seq($ori) if $ori; $aamut->allele_ori($a1); my $a2 = Bio::Variation::Allele->new; $a2->seq($mut) if $mut; $aachange->add_Allele($a2); $aachange->allele_mut($a2); print "\n"; # add it to a SeqDiff container object $seqdiff->add_Variant($rnachange); # and create links to and from RNA level variant objects $aamut->RNAChange($rnachange); $rnachange->AAChange($rnachange); The instantiable class Bio::Variation::RNAChange describes basic sequence changes at polypeptide level. It uses methods defined in superclass Bio::Variation::VariantI, see Bio::Variation::VariantI for details. If the variation described by a AAChange object has a known Bio::Variation::RNAAChange object, create the link with method AAChange(). See 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 _

RNAChange
Title : RNAChange Usage : $mutobj = $self->RNAChange; : $mutobj = $self->RNAChange($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

similarity_score
Title : similarity_score Usage : $self->similarity_score Function: Measure for evolutionary conservativeness of single amino substitutions. Uses BLOSUM62. Negative numbers are noncoservative changes. Returns : integer, undef if not single amino acid change

trivname
Title : trivname Usage : $self->trivname Function: Given a Bio::Variation::AAChange object with linked Bio::Variation::RNAChange and Bio::Variation::DNAMutation objects, this subroutine creates a string corresponding to the 'trivial name' of the mutation. Trivial 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