debian man page for bio::seqfeature::sirna::pair

Bio::SeqFeature::SiRNA::Pair(3pm)			User Contributed Perl Documentation			 Bio::SeqFeature::SiRNA::Pair(3pm)

NAME
       Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA (SiRNA) oligo pairs

SYNOPSIS
	 use Bio::SeqFeature::SiRNA::Pair;
	 my $pair = Bio::SeqFeature::SiRNA::Pair->
	     new( -sense       => $bio_seqfeature_sirna_oligo, # strand=1
		  -antisense   => $bio_seqfeature_sirna_oligo, # strand= -1
		  -primary     => 'SiRNA::Pair',
		  -source_tag  => 'Bio::Tools::SiRNA',
		  -start       => 8,
		  -end	       => 31,
		  -rank        => 1,
		  -fxgc        => 0.5,
		  -tag	       => { note => 'a note' } );

	 $target_sequence->add_SeqFeature($pair);

DESCRIPTION
       Object methods for (complementary) pairs of Bio::SeqFeature::SiRNA::Oligo objects - inherits Bio::SeqFeature::Generic. See that package for
       information on inherited methods.

       Does not include methods for designing SiRNAs -- see Bio::Tools::SiRNA

SEE ALSO
       Bio::SeqFeature::Oligo, Bio::Tools::SiRNA.

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)

APPENDIX
       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

METHODS
   new
	 Title	       : new
	 Usage	       : my $sirna_pair = Bio::SeqFeature::SiRNA::Pair->new();
	 Purpose       : Create a new SiRNA::Pair object
	 Returns       : Bio::Tools::SiRNA object
	 Args	       : -start        10
			 -end	       31
			 -rank	       1 #  'Rank' in Tuschl group's rules
			 -fxgc	       0.5 # GC fraction for target sequence
			 -primary      'SiRNA::Pair', # default value
			 -source_tag   'Bio::Tools::SiRNA'
			 -tag	       { note => 'A note' }
			 -sense        a Bio::SeqFeature::SiRNA::Oligo object
				       with strand = 1
			 -antisense    a Bio::SeqFeature::SiRNA::Oligo object
				       with strand = -1
       );

	 Note	       : SiRNA::Pair objects are typically created by a design
			 algorithm such as Bio::Tools::SiRNA

   rank
	 Title	       : rank
	 Usage	       : my $pair_rank = $sirna_pair->rank()
	 Purpose       : Get/set the 'quality rank' for this pair.
			 See Bio::Tools::SiRNA for a description of ranks.
	 Returns       : scalar
	 Args	       : scalar (optional) indicating pair rank

   fxGC
	 Title	       : fxGC
	 Usage	       : my $fxGC = $sirna_pair->fxGC();
	 Purpose       : Get/set the fraction of GC for this pair - based on TARGET sequence, not oligos.
	 Returns       : scalar between 0-1
	 Args	       : scalar between 0-1 (optional)

   sense
	 Title	       : sense
	 Usage	       : my $sense_oligo = $sirna_pair->sense()
	 Purpose       : Get/set the SiRNA::Oligo object corresponding to the sense strand
	 Returns       : Bio::SeqFeature::SiRNA::Oligo object
	 Args	       : Bio::SeqFeature::SiRNA::Oligo object

   antisense
	 Title	       : antisense
	 Usage	       : my $antisense_oligo = $sirna_pair->antisense()
	 Purpose       : Get/set the SiRNA::Oligo object corresponding to the antisense strand
	 Returns       : Bio::SeqFeature::SiRNA::Oligo object
	 Args	       : Bio::SeqFeature::SiRNA::Oligo object

perl v5.14.2							    2012-03-02					 Bio::SeqFeature::SiRNA::Pair(3pm)