Bio::Variation::AAReverseMutate(3pm)			User Contributed Perl Documentation		      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, "
";
	      }
	  } else  {
	      print "No point mutations possible
",
	  }

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

perl v5.14.2							    2012-03-02				      Bio::Variation::AAReverseMutate(3pm)