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01-17-2012
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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)