Bio::Tools::SiRNA::RulUser:Contributed PerBio::Tools::SiRNA::Ruleset::saigo(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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
perl v5.14.12011-07-Bio::Tools::SiRNA::Ruleset::saigo(3)