$max_seqs ) : ?>
You can input no more than sequences at a time.
" . $v['name'] . "\n" . substr($v['seq'], -60) ."\n";
}
echo $input;
file_put_contents( $file, $input );
chdir("./juchmme/bin");
#Arxaia
if($organism=='arc')
{
exec ("java hmm/Juchmme -a ../tables/A_archaea_trained -e ../tables/E_archaea_trained -c ../conf/conf.cwpred_archaea -m ../models/cwpred_archaea.mdel -f $file -p", $out, $ret);
}
#Gram-negative
elseif ($organism=='neg')
{
exec("java hmm/Juchmme -a ../tables/A_negative_trained -e ../tables/E_negative_trained -c ../conf/conf.cwpred_negative -m ../models/cwpred_negative.mdel -f $file -p", $out, $ret);
}
#Gram-posiive
elseif ($organism=='pos')
{
exec("java hmm/Juchmme -a ../tables/A_positive_trained -e ../tables/E_positive_trained -c ../conf/conf.cwpred_positive -m ../models/cwpred_positive.mdel -f ../input/positive_training.txt -f $file -p", $out, $ret);
}
unlink( $file );
chdir("../../");
?>
$out";
preg_match_all( '/Preparing Sequences.*?LP: \w*/s', $out, $matches );
$results = $matches[0];
#print "
LALAKIS
$results
";
?>
$r
";
preg_match( '/^ID: >(.*)$/m', $r, $matches );
$seq_name = $matches[1];
preg_match( '/^VP: (.*)$/m', $r, $matches );
$reliability = $matches[1];
preg_match_all( '/\d+\s*\((.)\)\s*.:\s*VI:\s*(.)\s*PVI:\s*.\s*PVI:\s*.\s*\|.*\|.*\|.*\|.*\|.*\|\s*([\d\.E-]*)\s*([\d\.E-]*)\s*([\d\.E-]*)\s*([\d\.E-]*)\s*([\d\.E-]*)/', $r, $matches );
for( $i=3; $i<=7; $i++ ) {
$arr = array();
foreach( $matches[$i] as $v ) {
$arr[] = round($v, $precision);
}
$paths[] = $arr;
}
$aa = $matches[1];
$vpath = $matches[2];
?>
![](http://chart.apis.google.com/chart?<?= "chs=600x200" .
"&cht=lc" .
"&chco=FF0000,00FF00,0000FF" . // ",FF00FF,00FFFF" .
"&chds=0,1,0,1,0,1" . // ",0,1,0,1" .
"&chdl=Lipo signal peptide|Sec signal peptide|TM segment" .
"&chxt=x,x,y,y".
"&chxr=2,0,1|0,1,".count($aa).
"&chxl=3:|Posterior probability|1:|Residue no". //implode()
' />
$v ) {
if( $v != $previous ) {
if( $v == 'S' || $v == 'M') {
$start = $k+1;
if( $v== 'S' )
$type = 'Sec signal peptide';
elseif( $v== 'M' )
$type = 'TM segment';
} else {
$end = $k;
}
}
$previous = $v;
}
#$cleavage = $aa[$end-3] . $aa[$end-2] . $aa[$end-1] ."-". $aa[$end-0] . $aa[$end+1];
?>
': ' - ' ?>
predicted.
No cell-wall sorting signal detected
': ' - ' ?>
Reliability score:
Program execution error. Please contact us for help.
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Please paste up to sequences in the textarea below:
If you find CW-PRED useful in your research, please consider citing the reference that describes this work:
A Hidden Markov Model for the prediction of C-terminal cell-wall sorting signals in Bacteria and Archaea.
Aikaterini G. Chatziargyri¶ , Evangelia A. Stasi¶ , Eleni Nydrioti, Konstantinos D. Tsirigos, Zoi I. Litou, Vassiliki A. Iconomidou and Pantelis G. Bagos.
under review