NAME¶
Bio::Tools::SiRNA::Ruleset::saigo - Perl object implementing the Saigo group's
rules for designing small inhibitory RNAs
SYNOPSIS¶
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";
}
DESCRIPTION¶
This package implements the rules for designing siRNA reagents published by
Ui-Tei et al (2004). The rules are:
- 1.
- The first base in the sense strand of the duplex must be a
G or C
- 2.
- The first base in the antisense strand of the duplex must
be an A or U
- 3.
- The first 7 nucleotides in the antisense strand of the
duplex must be A or U
- 4.
- There cannot be more than 9 consecutive G or C
nucleotides
- 5.
- The first 12 nucleotides in the sense strand of the duplex
should have 33-66% GC
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.
EXPORT¶
None.
SEE ALSO¶
Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair, Bio::SeqFeature::SiRNA::Oligo.
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
list. 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 of the bugs
and their resolution. Bug reports can be submitted via the web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR¶
Donald Jackson (donald.jackson@bms.com)
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
new¶
Title : new
Usage : Do not call directly - use Bio::Tools::SiRNA->new instead.
Returns : Bio::Tools::SiRNA::Ruleset::saigo object
Args : none