bio::tools::sirna::ruleset::saigo(3pm) [debian man page]
Bio::Tools::SiRNA::Ruleset::saigo(3pm) User Contributed Perl Documentation Bio::Tools::SiRNA::Ruleset::saigo(3pm) 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 (" ", $pair->start, $pair->end, $pair->rank, $sense_oligo_sequence, $antisense_oligo_sequence), " "; } 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 perl v5.14.2 2012-03-02 Bio::Tools::SiRNA::Ruleset::saigo(3pm)
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Bio::SeqFeature::SiRNA::Pair(3pm) User Contributed Perl Documentation Bio::SeqFeature::SiRNA::Pair(3pm) NAME
Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA (SiRNA) oligo pairs SYNOPSIS
use Bio::SeqFeature::SiRNA::Pair; my $pair = Bio::SeqFeature::SiRNA::Pair-> new( -sense => $bio_seqfeature_sirna_oligo, # strand=1 -antisense => $bio_seqfeature_sirna_oligo, # strand= -1 -primary => 'SiRNA::Pair', -source_tag => 'Bio::Tools::SiRNA', -start => 8, -end => 31, -rank => 1, -fxgc => 0.5, -tag => { note => 'a note' } ); $target_sequence->add_SeqFeature($pair); DESCRIPTION
Object methods for (complementary) pairs of Bio::SeqFeature::SiRNA::Oligo objects - inherits Bio::SeqFeature::Generic. See that package for information on inherited methods. Does not include methods for designing SiRNAs -- see Bio::Tools::SiRNA SEE ALSO
Bio::SeqFeature::Oligo, Bio::Tools::SiRNA. 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 _ METHODS
new Title : new Usage : my $sirna_pair = Bio::SeqFeature::SiRNA::Pair->new(); Purpose : Create a new SiRNA::Pair object Returns : Bio::Tools::SiRNA object Args : -start 10 -end 31 -rank 1 # 'Rank' in Tuschl group's rules -fxgc 0.5 # GC fraction for target sequence -primary 'SiRNA::Pair', # default value -source_tag 'Bio::Tools::SiRNA' -tag { note => 'A note' } -sense a Bio::SeqFeature::SiRNA::Oligo object with strand = 1 -antisense a Bio::SeqFeature::SiRNA::Oligo object with strand = -1 ); Note : SiRNA::Pair objects are typically created by a design algorithm such as Bio::Tools::SiRNA rank Title : rank Usage : my $pair_rank = $sirna_pair->rank() Purpose : Get/set the 'quality rank' for this pair. See Bio::Tools::SiRNA for a description of ranks. Returns : scalar Args : scalar (optional) indicating pair rank fxGC Title : fxGC Usage : my $fxGC = $sirna_pair->fxGC(); Purpose : Get/set the fraction of GC for this pair - based on TARGET sequence, not oligos. Returns : scalar between 0-1 Args : scalar between 0-1 (optional) sense Title : sense Usage : my $sense_oligo = $sirna_pair->sense() Purpose : Get/set the SiRNA::Oligo object corresponding to the sense strand Returns : Bio::SeqFeature::SiRNA::Oligo object Args : Bio::SeqFeature::SiRNA::Oligo object antisense Title : antisense Usage : my $antisense_oligo = $sirna_pair->antisense() Purpose : Get/set the SiRNA::Oligo object corresponding to the antisense strand Returns : Bio::SeqFeature::SiRNA::Oligo object Args : Bio::SeqFeature::SiRNA::Oligo object perl v5.14.2 2012-03-02 Bio::SeqFeature::SiRNA::Pair(3pm)