Bio::Variation::AAChange(3)

NAME
Bio::Variation::AAChange - Sequence change class for polypeptides

SYNOPSIS
   $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);

DESCRIPTION
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.

FEEDBACK

  Mailing Lists
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  bioperl-l@bioperl.org                         - General discussion
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  http://bugzilla.bioperl.org/

AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk

Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

APPENDIX
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