Bio::Tools::SiRNA::Ruleset::tuschl(3pm) | User Contributed Perl Documentation | Bio::Tools::SiRNA::Ruleset::tuschl(3pm) |
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
2018-10-27 | perl v5.26.2 |