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:

https://github.com/bioperl/bioperl-live/issues

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