04-03-2010
Quote:
Hi.
I don't understand your response. Are you using a completely different format for the data file, is the problem solved, or what? ... cheers, drl
I guess it is a different format. Here are few lines of the data:
data1
>chr1_12 strand:+ excise_beg:16047184 excise_end:16047293
ACTTACCCGAGAACGTGCGGGAAGAGAAGATCATCGAGCATTTCAAACGGTGAGTGACACG
>chr13_124 strand:+ excise_beg:16047141 excise_end:16047250
CCGCCCAGCATGGTCCGGGAAACCAGGCATCTCTGGGTGGGCAACTTACCCGAGAACGTGCG
>chr9_2 strand:+ excise_beg:44109537 excise_end:44109646
AGGGGACCAGAAGAACCCTGGTAGAGAACTCAGGAGAAGGAGGCTAGGAA
data2
chr1_12
chr13_124
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LEARN ABOUT DEBIAN
bio::tools::sirna::ruleset::saigo
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)