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)