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¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  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 _

  Title : new
  Usage : Do not call directly - use Bio::Tools::SiRNA->new instead.
  Returns : Bio::Tools::SiRNA::Ruleset::saigo object
  Args  : none