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]

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 ([email protected])

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