NAME

       Bio::Variation::AAReverseMutate - point mutation and codon
         information from single amino acid changes

SYNOPSIS

           $aamut = Bio::Variation::AAReverseMutate->new
                        (-aa_ori => 'F',
                         -aa_mut => 'S',
                         -codon_ori => 'ttc', # optional
                         -codon_table => '3'  # defaults to 1
                         );

          @points = $aamut->each_Variant;

          if (scalar @points > 0 ) {
              foreach $rnachange ( @points ) {
                  # $rnachange is a Bio::Variation::RNAChange object
                  print " ", $rnachange->allele_ori->seq, ">",
                  $rnachange->allele_mut->seq, " in ",
                  $rnachange->codon_ori, ">", $rnachange->codon_mut,
                  " at position ", $rnachange->codon_pos, "\n";
              }
          } else  {
              print "No point mutations possible\n",
          }

DESCRIPTION

       Bio::Variation::AAReverseMutate objects take in reference and mutated amino acid
       information and deduces potential point mutations at RNA level leading to this change. The
       choice can be further limited by letting the object know what is the the codon in the
       reference sequence. The results are returned as Bio::Variation::RNAChange objects.

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://redmine.open-bio.org/projects/bioperl/

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 _

   aa_ori
        Title   : aa_ori
        Usage   : $obj->aa_ori();
        Function:

                   Sets and returns original aa sequence.  If value is not
                   set, returns false.

                   Amino acid sequences are stored in upper case characters,
                   others in lower case.

        Example :
        Returns : string
        Args    : single character amino acid code

   aa_mut
        Title   : aa_mut
        Usage   : $obj->aa_mut();
        Function:

                   Sets and returns the mutated allele sequence.  If value is not
                   set, returns false.

        Example :
        Returns : string
        Args    : single character amino acid code

   codon_ori
        Title   : codon_ori
        Usage   : $obj->codon_ori();
        Function:

                   Sets and returns codon_ori triplet.  If value is not set,
                   returns false.  The string has to be three characters
                   long. The chracter content is not checked.

        Example :
        Returns : string
        Args    : string

   codon_table
        Title   : codon_table
        Usage   : $obj->codon_table();
        Function:

                   Sets and returns the codon table id of the RNA
                   If value is not set, returns 1, 'universal' code, as the default.

        Example :
        Returns : integer
        Args    : none if get, the new value if set

   each_Variant
        Title   : each_Variant
        Usage   : $obj->each_Variant();
        Function:

                   Returns a list of Variants.

        Example :
        Returns : list of Variants
        Args    : none