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Bio::Variation::AAChange.3pm

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

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.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

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 the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

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.
 
  Returns : string