GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::SEQFEATURE::SIRNA::PAIR (3)

.ds Aq ’

NAME

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

CONTENTS

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 <B>notB> 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://github.com/bioperl/bioperl-live/issues



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 groups 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



Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::SEQFEATURE::SIRNA::PAIR (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.