Bio::Tools::SiRNA::Ruleset tuschl
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Summary
Bio::Tools::SiRNA::Ruleset::tuschl - Perl object implementing the
tuschl group's rules for designing small inhibitory RNAs
Package variables
No package variables defined.
Inherit
Bio::Tools::SiRNA
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, $antisense_oligo_sequence), "\n"; }
Description
This package implements the rules for designing siRNA reagents
developed by Tuschl and colleagues (see
http://www.rockefeller.edu/labheads/tuschl/sirna.html). It looks for
oligos that match the following patterns in the target sequence:
  1. AA(N19)TT (rank 1)
2. AA(N21) (rank 2)
3. NA(N21) (rank 3)
The package also supports selection of siRNA seqences that can be
transcribed by pol3:
    A[A,G]N17[C,T]
Methods
newDescriptionCode
_regex
No description
Code
cutoff
No description
Code
_get_oligos
No description
Code
_get_sense
No description
Code
_get_anti
No description
Code
Methods description
newcode    nextTop
  Title	: new
Usage : Do not call directly - use Bio::Tools::SiRNA->new instead.
Returns : Bio::Tools::SiRNA::Ruleset::saigo object
Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my ($proto, %args) = @_;
    my $class = ref($proto) || $proto;
    
    $args{'RULES'} = 'tuschl';

    return $class->SUPER::new(%args);
}
_regexdescriptionprevnextTop
sub _regex {
    my ($self, $rank) = @_;
    return $PATTERNS{$rank};
}
cutoffdescriptionprevnextTop
sub cutoff {
    my ($self, $cutoff) = @_;
    if ($cutoff) {
	$self->{'cutoff'} = $cutoff;
    }
    elsif (!$self->{'cutoff'}) {
	$self->{'cutoff'} = $DEFAULT_CUTOFF;
    }
    return $self->{'cutoff'};
}
_get_oligosdescriptionprevnextTop
sub _get_oligos {
    #use regular expressions to pull out oligos
my ($self) = @_; my @ranks; if ($self->cutoff eq 'pol3') { @ranks = ('pol3'); } else { @ranks = (1 .. $self->cutoff); } foreach my $rank (@ranks) { my $regex = $self->_regex($rank); #my @exclude;
# my ($targregion) = grep { $_->primary_tag eq 'Target' } $self->target->top_SeqFeatures;
# my $seq = $targregion->seq->seq;
# # but this way I loose start info
# my $targstart = $targregion->start;
my ($seq, $targstart) = $self->_get_targetregion(); while ( $seq =~ /(.*?)$regex/gi ) { my $target = $2; # check for too many Gs (or Cs on the other strand)
next if ( $target =~ /G{ $self->gstring,}/io ); next if ( $target =~ /C{ $self->gstring,}/io ); # skip Ns (for filtering)
next if ( $target =~ /N/i); my $start = length($1) + $targstart; my $stop = $start + length($target) -1; my @gc = ( $target =~ /G|C/gi); my $fxGC = sprintf("%2.2f", (scalar(@gc) / length($target)));
next if ($fxGC < $self->min_gc); next if ($fxGC > $self->max_gc); $self->add_oligos($target, $start, $rank); } }
}
_get_sensedescriptionprevnextTop
sub _get_sense {
    my ($self, $target) = @_;
    # trim off 1st 2 nt to get overhang
$target =~ s/^..//; # convert T's to U's (transcribe)
$target =~ s/T/U/gi; # force last 2 nt to be T's
$target =~ s/..$/TT/; return $target;
}
_get_antidescriptionprevnextTop
sub _get_anti {
    my ($self, $target) = @_;
    my @target = split(//, $target);
    my ($nt,@antitarget);

    while ($nt = pop @target) {
	push(@antitarget, $self->_comp($nt));
    }
    my $anti = join('', @antitarget);
    # trim off 1st 2 nt to get overhang
$anti =~ s/^..//; # convert T's to U's
$anti =~ s/T/U/gi; # convert last 2 NT's to T
$anti =~ s/..$/TT/; return $anti; } 1;
}
General documentation
SEE ALSOTop
Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair,
Bio::SeqFeature::SiRNA::Oligo.
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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/
AUTHORTop
Donald Jackson (donald.jackson@bms.com)
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _