Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::Tools::SiRNA::RulUser:Contributed PeBio::Tools::SiRNA::Ruleset::tuschl(3)

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

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

	 use Bio::Tools::SiRNA;

	 my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq,
						      -rules  => 'tuschl'
	   );
	 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
       developed by Tuschl and colleagues (see
       http://www.rockefeller.edu/labheads/tuschl/sirna.html). It looks	for
       oligos that match the following patterns	in the target sequence:

	 1. AA(N19)TT (rank 1)
	 2. AA(N21) (rank 2)
	 3. NA(N21) (rank 3)

       The package also	supports selection of siRNA seqences that can be
       transcribed by pol3:

	   A[A,G]N17[C,T]

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://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 _

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

perl v5.24.1			  2017-07Bio::Tools::SiRNA::Ruleset::tuschl(3)

NAME | SYNOPSIS | DESCRIPTION | SEE ALSO | FEEDBACK | AUTHOR | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Tools::SiRNA::Ruleset::tuschl&sektion=3&manpath=FreeBSD+12.0-RELEASE+and+Ports>

home | help