Christopher Fields > BioPerl-1.6.922 > Bio::Tools::SiRNA::Ruleset::saigo

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Module Version: 1.006922   Source   Latest Release: BioPerl-1.6.924

NAME ^

Bio::Tools::SiRNA::Ruleset::saigo - Perl object implementing the Saigo group's rules for designing small inhibitory RNAs

SYNOPSIS ^

Do not use this module directly. Instead, use Bio::Tools::SiRNA and specify the saigo ruleset:

  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 ^

This package implements the rules for designing siRNA reagents published by Ui-Tei et al (2004). The rules are:

  1. The first base in the sense strand of the duplex must be a G or C
  2. The first base in the antisense strand of the duplex must be an A or U
  3. The first 7 nucleotides in the antisense strand of the duplex must be A or U
  4. There cannot be more than 9 consecutive G or C nucleotides
  5. The first 12 nucleotides in the sense strand of the duplex should have 33-66% GC

The module inherits from Bio::Tools::SiRNA. See the documentation for that module for information on how to specify the target and recover the SiRNA duplex information.

EXPORT

None.

SEE ALSO ^

Bio::Tools::SiRNA, 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:

  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 _

new

  Title : new
  Usage  : Do not call directly - use Bio::Tools::SiRNA->new instead.
  Returns : Bio::Tools::SiRNA::Ruleset::saigo object
  Args  : none
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