/ 
bioperl-1.5.2_004-RCd
/ Bio::SeqFeature::SiRNA::Pair

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

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 _

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