Bio::Tools::SiRNA::Ruleset::tuschl - Perl object implementing the tuschl group's rules for designing small inhibitory RNAs
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"; }
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]
Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair, Bio::SeqFeature::SiRNA::Oligo.
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.
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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/
Donald Jackson (donald.jackson@bms.com)
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : Do not call directly - use Bio::Tools::SiRNA->new instead. Returns : Bio::Tools::SiRNA::Ruleset::saigo object Args : none
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.