bionic (3) Bio::Tools::SiRNA::Ruleset::tuschl.3pm.gz

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