view release on metacpan or  search on metacpan

examples/sirna/rnai_finder.cgi  view on Meta::CPAN

my $NOLIGOS = 3;

my $log = $TMPDIR . 'RNAiFinder.log';
open (LOG, ">>$log") or die $!;
carpout(LOG);

print $q->header,
    $q->start_html;
    
print $q->h1('RNAi Finder');


if ($q->param('Design')) {
    if ($q->param('accession') and !$q->param('seq')) {
	$target = get_target();
    }
    else { 
	$target = make_target();
    }
    get_rnai($target);
}
else {
    get_settings();
}


sub get_settings {
    print <<EOM1;
<P>Oligos are designed as described on the <A HREF="http://www.mpibpc.gwdg.de/abteilungen/100/105/sirna.html" TARGET="Tuschl">Tuschl lab web page</A> and are ranked as follows: 
<UL>
<LI><B>New:</B> Selecting 'Pol3-compatible targets' looks for oligos with the 
pattern NAR(N17)YNN which can be synthesized or expressed from a Pol3 promoter.
<br>This selection <b>overrides</b> the 'Cutoff' rank.
<LI>Oligos with Rank = 1 (best) match the AAN(19)TT rule.
<LI>Oligos with Rank = 2 match the AAN(21) rule 
<LI>Oligos with Rank = 3 match the NAN(21) rule.
</UL>
<P>If percent GC and specificity are similar, Rank 1 oligos are better. All 3 prime overhangs are converted to TT; the rest of the sequence is transcribed into RNA</P>

<h3>Modifications to published rules:</h3>
<ul>
<li>
Runs of 3 or more consecutive Gs on either strand are skipped - these can cause problems in synthesis. 
<li>Users may choose to exclude oligos that overlap single nucleotide polymorphisms (ON by default).  SNP data comes from the NCBI dbSNP database.  
<li>'Low-complexity' regions (such as runs of a single nucleotide) are also excluded.
</ul>

EOM1
    
    print $q->start_form;
    print $q->h2('Enter your sequence and other parameters:'), "\n";
    print $q->p('The values already here are DEFAULTS - you should change them to suit YOUR sequence');
    print $q->start_table();
    print $q->TR( $q->td({-align=> 'left'}, 
		       [
			$q->textfield(-name 	=> 'mingc', -default => '0.40'),
			$q->textfield(-name 	=> 'maxgc', -default => '0.60'),
			]
		       ),
		      $q->td({-align=> 'left'},
			     $q->popup_menu(-name	 => 'worstrank', 
				      -values 	=> [1,2,3], 
				      -default 	=> 2,
				      ),
			     $q->b('OR'),
			     $q->checkbox(-name 		=> 'pol3',
				    -label		=> 'Pol3 compatible',
				    -default	=> 0,
				    ),
			     ),
		      );	
    print    $q->TR( $q->th({-align=> 'left'}, 'Exclude oligos with SNPs?'),
		     $q->td($q->radio_group(-name => 'avoid_snps', 
					    -values => [1,0],
					    -default => 1,
					    -labels => {1 => 'Yes', 0 => 'No'}
					    )),
		     );

    print $q->TR( $q->th({-align=> 'left'}, 'Sequence Name:'),
		  $q->td({-align=> 'left'},$q->textfield('accession')),
		  $q->td({-align=> 'left'}, 
			 $q->em( q(Enter an accession and you won't have to enter the <br>sequence or start/stop. Use accessions beginning with NM_ if possible.))),
		  );

    print $q->TR( $q->th({-align=> 'left'}, ['Position of initiator ATG:', 
					     'NT after start to exclude:',
					     'Position of Stop codon:' ]));
    print $q->TR( $q->td({-align=> 'left'}, 
					   [$q->textfield(-name => 'cdstart', -default => 1),
					    $q->textfield(-name => 'atgpad', -default => $ATGPAD),
					    $q->textfield('cdend'), ]));
    print $q->TR( $q->th({-align=> 'left'}, ['Minimum Fraction GC:', 
					     'Maximum Fraction GC:', 
					     'Rank cutoff',
					     ]));
    print $q->TR($q->th({-align=> 'left', -colspan=>2},'cDNA Sequence in plain text or FASTA format'),
		 $q->td( $q->a({-href =>'Fasta_format.html', -target => 'Fasta_desc'}, 'What is FASTA format?')),
		 );
    print $q->TR($q->td({-align => 'left', -colspan=>3},
		  $q->textarea( -name =>'seq',
				-rows => 4,
				-columns => 80, 
				-wrap => 'virtual',
				)));
    print $q->TR( $q->th({-align => 'left', -colspan=>3},
			 'Output options: '));
    print $q->TR( $q->td({-align=> 'left'},
		   [ $q->checkbox(-name => 'Graphic', -checked => 'checked'), 
		     $q->checkbox(-name =>  'Table',  -checked => 'checked'), 
						 ]));			       		   		
    print $q->TR($q->td({-align=> 'left', -colspan=>3}, $q->submit('Design')));
    print $q->end_table();		
    print $q->end_form;

}

sub get_rnai {
    # design and output RNAi reagents
    my ($gene) = @_;