Bio::Tools::SiRNA::RulUser:Contributed PeBio::Tools::SiRNA::Ruleset::tuschl(3)NAMEBio::Tools::SiRNA::Ruleset::tuschl - Perl object implementing the
tuschl group's rules for designing small inhibitory RNAs
SYNOPSIS
Do not use this module directly. Instead, use Bio::Tools::SiRNA and
specify the tuschl ruleset:
use Bio::Tools::SiRNA;
my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq,
-rules => 'tuschl'
);
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
developed by Tuschl and colleagues (see
http://www.rockefeller.edu/labheads/tuschl/sirna.html). It looks for
oligos that match the following patterns in the target sequence:
1. AA(N19)TT (rank 1)
2. AA(N21) (rank 2)
3. NA(N21) (rank 3)
The package also supports selection of siRNA seqences that can be
transcribed by pol3:
A[A,G]N17[C,T]
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 v5.14.12011-07Bio::Tools::SiRNA::Ruleset::tuschl(3)
