Bio::SeqFeature::SiRNA::Pair.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   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