Bio::Tools::SiRNA::Ruleset::saigo - Perl object implementing the Saigo

  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";
  }

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://redmine.open-bio.org/projects/bioperl/

  Title	: new
  Usage  : Do not call directly - use Bio::Tools::SiRNA->new instead.
  Returns : Bio::Tools::SiRNA::Ruleset::saigo object
  Args	: none

# BioPerl module for Bio::Tools::SiRNA::Ruleset::saigo
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Donald Jackson, donald.jackson@bms.com
#
# Copyright Bristol-Myers Squibb
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

package Bio::Tools::SiRNA::Ruleset::saigo;

use strict;
use warnings;

use base qw(Bio::Tools::SiRNA);

sub new {
    my ($proto, %args) = @_;
    my $class = ref($proto) || $proto;
    
    $args{'RULES'} = 'saigo';
    
    return $class->SUPER::new(%args);
 }

sub _get_oligos {
    my ($self) = @_;

    my ($targseq, $targstart) = $self->_get_targetregion;

    foreach my $i (0 .. (length($targseq) - 23)) {
	my $testseq = substr($targseq, $i, 23);		
	$self->add_oligos($testseq, $targstart + $i + 1) if ($self->_oligo_ok($testseq));
    }
}


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;

    return $target;
}

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;

    return $anti;
}

sub _oligo_ok {
    my ($self, $testseq) = @_;

    $self->debug("Testing $testseq...\n");

    my @testseq = split(//, $testseq);
    # is 5p end of sense strand a G/C?
    unless ($testseq[2] =~ /[GC]/i) {
	$self->debug("No G/C at sense 5' end\n");
	return 0;
    }
    # is 5p end of antisense strand an A/T?
    unless ($testseq[20] =~ /[AT]/i) {
	$self->debug("No A/T at antisense 5' end\n");
	return 0;
    }

    # are 4 of the last 7 bases in the duplex A/T?
    my $atcount_3p = grep { /[AT]/i } @testseq[14 .. 20];
    unless ($atcount_3p >= 4) {
	$self->debug("Found $atcount_3p A/T in last 7 bases of duplex\n");
	return 0;
    }
    # what is gc fraction in rest of duplex? Target: 33 to 66 pct gc (4-8 of 12)
    my $gccount_5p = grep { /[GC]/i } @testseq[2 .. 13];
    if ($gccount_5p < 4) {
	$self->debug("Found only $gccount_5p GCs in 5p end of duplex\n");
	return 0;
    }
    if ($gccount_5p > 8) {
	$self->debug("Found only $gccount_5p GCs in 5p end of duplex\n");
	return 0;
    }
    
    # no more than 9 consecutive GC
    if ($testseq =~ /[GC]{9,}?/i) {
	$self->debug("Found more than 9 consecutive GCs\n");
	return 0;
    }

    $self->debug("Oligo passed \n");
    return 1;
}

1;