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Bio::Variation::AAReverseMutate.3pm

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:

   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 _

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