NAME¶
Bio::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:
https://github.com/bioperl/bioperl-live/issues
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