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Bio::Tools::SiRNA(3)  User Contributed Perl Documentation Bio::Tools::SiRNA(3)

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)

perl v5.14.1			  2011-07-22		  Bio::Tools::SiRNA(3)
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