Bio::Variation::AAReverseMutate - point mutation and codon information from single amino acid changes $aamut = new Bio::Variation::AAReverseMutate (-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", } 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 the Bio::Variation::RNAChange manpage objects.

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom 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 information from single amino acid changes"