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Bio::Tools::SiRNA.3pm

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.

SEE ALSO

Bio::Tools::Run::Mdust, 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:

   http://bugzilla.open-bio.org/
 
 

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          : my $sirna_designer = Bio::Tools::SiRNA->new();
  Function       : Constructor for designer object
  Returns        : Bio::Tools::SiRNA object
  Args           : target - the target sequence for the SiRNAs as a Bio::Seq::RichSeq
                   start_pad - distance from the CDS start to skip (default 75)
                   end_pad - distance from the CDS end to skip (default 50)
                   include_3pr - set to true to include SiRNAs in the 3prime UTR (default false)
                   rules - rules for selecting siRNAs, currently supporting saigo and tuschl
                   min_gc - minimum GC fraction (NOT percent) (default 0.4)
                   max_gc - maximum GC fraction (NOT percent) (default 0.6)
                   cutoff - worst 'rank' accepted(default 3)
                   avoid_snps - boolean - reject oligos that overlap a variation
                      SeqFeature in the target (default true)
                   gstring - maximum allowed consecutive Gs.
                      Too many can cause problems in synthesis (default 4)
   Note          : All arguments can also be changed/accessed using autoloaded 
                  methods such as:
 
     my $start_pad = $sirna_designer->start_pad().
 
 

target

   Title         : target
   Usage         : my $target_seq = $sirna_designer->target(); # get the current target
                   OR 
                   $sirna_designer->target($new_target_seq); # set a new target 
   Function      : Set/get the target as a Bio::SeqI-compliant object
   Returns       : a Bio::SeqI-compliant object
   Args          : a Bio::SeqI-compliant object (optional)
 
 

rules

     Title       : rules
     Usage       : $sirna->rules('ruleset')
     Purpose     : set/get ruleset to use for selecting SiRNA oligo pairs.
     Returns     : not sure yet
     Args        : a ruleset name (currently supported: Tuschl, Saigo)
                   or a Bio::Tools::SiRNA::RulesetI compliant object
 
 

design

   Title         : design
   Usage         : my @pairs = $sirna_designer->design();
   Purpose       : Design SiRNA oligo pairs.  
   Returns       : A list of SiRNA pairs as Bio::SeqFeature::SiRNA::Pair objects
   Args          : none
 
 

add_oligos

   Title         : add_oligos
   Usage         : $sirna_designer->add_oligos($sequence, $start, $rank);
   Purpose       : Add SiRNA olgos to target Bio::Seq as Bio::SeqFeature::SiRNA::Pair objects
   Args          : Oligo sequence and start position (required), rank/score (optional)