Bio::Tools::SiRNA::Ruleset::saigo(3pm) | User Contributed Perl Documentation | Bio::Tools::SiRNA::Ruleset::saigo(3pm) |
Bio::Tools::SiRNA::Ruleset::saigo - Perl object implementing the Saigo group's rules for designing small inhibitory RNAs
Do not use this module directly. Instead, use Bio::Tools::SiRNA and specify the saigo ruleset:
use Bio::Tools::SiRNA; my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq, -rules => 'saigo' ); my @pairs = $sirna_designer->design; foreach $pair (@pairs) { my $sense_oligo_sequence = $pair->sense->seq; my $antisense_oligo_sequence = $pair->antisense->seq; # print out results print join ("\t", $pair->start, $pair->end, $pair->rank, $sense_oligo_sequence, $antisense_oligo_sequence), "\n"; }
This package implements the rules for designing siRNA reagents published by Ui-Tei et al (2004). The rules are:
The module inherits from Bio::Tools::SiRNA. See the documentation for that module for information on how to specify the target and recover the SiRNA duplex information.
None.
Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair, Bio::SeqFeature::SiRNA::Oligo.
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 list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
Donald Jackson (donald.jackson@bms.com)
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : Do not call directly - use Bio::Tools::SiRNA->new instead. Returns : Bio::Tools::SiRNA::Ruleset::saigo object Args : none
2018-10-27 | perl v5.26.2 |