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Bio::Variation::AAReveUseruContributed Perl Bio::Variation::AAReverseMutate(3)

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://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 _

   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 character 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 v5.32.0			  2020-01-06Bio::Variation::AAReverseMutate(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Heikki Lehvaslaiho | APPENDIX

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