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.
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.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
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. Returns : string