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

Provided by: libbio-perl-perl_1.6.924-3_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://github.com/bioperl/bioperl-live/issues

AUTHOR

       Donald Jackson (donald.jackson@bms.com)

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