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Bio::Tools::SiRNA::Ruleset::saigo.3pm
Langue: en
Version: 2009-03-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Tools::SiRNA::Ruleset::saigo - Perl object implementing the Saigo group's rules for designing small inhibitory RNAsSYNOPSIS
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
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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:http://bugzilla.open-bio.org/
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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