Ubuntu Manpage: SiRNA - Perl object for designing small inhibitory RNAs.

Provided by: libbio-perl-perl_1.6.923-1_all

NAME

       SiRNA - Perl object for designing small inhibitory RNAs.

SYNOPSIS

         use Bio::Tools::SiRNA;

         my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq,
                                                      -rules  => 'saigo'
           );
         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

Package for designing siRNA reagents.

Input is a Bio::SeqI-compliant object (the target).

Output is a list of Bio::SeqFeature::SiRNA::Pair objects, which are added to the feature table of the
target sequence. Each Bio::SeqFeature::SiRNA::Pair contains two subfeatures (Bio::SeqFeature::Oligo
objects) which correspond to the individual oligos. These objects provide accessors for the information
on the individual reagent pairs.

This verion of Bio::Tools::SiRNA represents a major change in architecture. Specific 'rulesets' for
siRNA selection as developed by various groups are implemented as Bio::Tools::SiRNA::Ruleset objects,
which inherit from Bio::Tools::SiRNA. This will make it easier to add new rule sets or modify existing
approaches. Currently the Tuschl and Ui-Tei (2004) rules are implemented. For consistency, the Tuschl
rules are implemented by default.

In addition, this module provides three 'extra' rules which can be added above and beyond any ruleset.

1. SiRNAs that overlap known SNPs (identified as SeqFeatures with primary tag = variation) can be
avoided.

2. Other regions (with primary tag = 'Excluded') can also be skipped. I use this with
Bio::Tools::Run::Mdust to avoid low-complexity regions (must be run separately), but other programs
could also be used.

3. SiRNAs may also be selected in the 3 prime UTR of a gene by setting $sirna_designer->include_3pr() to
true.

EXPORT
None.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Donald Jackson (donald.jackson@bms.com)

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