2500){die("Error:
In this demo, input sequence is limited to 2.500 characters.");}
$sequence=preg_replace("/\\W|\\d/","",$sequence);
// maximum length of amplicons
$maxlength=$_POST["length"];
// SET PATTERNS FROM PRIMERS
// Change N to point in primers
$pattern1=str_replace("N", ".", $primer1);
$pattern2=str_replace("N", ".", $primer2);
// If one missmatch is allowed, create new pattern
// example: pattern="ACGT"; to allow one missmatch pattern=".CGT|A.GT|AC.T|ACG."
if ($_POST["allowmissmatch"]==1){
$pattern1=includeN($primer1);
$pattern2=includeN($primer2);
}
// SET PATTERN
$start_pattern="$pattern1|$pattern2";
$end_pattern=RevComp($start_pattern);
// CALL Amplify FUNCTION
$results_array=Amplify($start_pattern,$end_pattern,$sequence,$maxlength);
// PRINT RESULTS
print "Primer 1: $primer1\\n";
print "Primer 2: $primer2\\n\\n";
if (sizeof($results_array)>0){
print "List of amplicons: position in sequence, length and sequence\\n\\n";
foreach($results_array as $key => $val){
print "$key $val ".substr($sequence,$key,$val)."\\n";
}
}else{
print "No amplification\\n\\n";
}
// ##############################################################
// FUNCTIONS
// ##############################################################
function Amplify ($start_pattern,$end_pattern,$sequence,$maxlength){
// SPLIT SEQUENCE BASED IN $start_pattern (start positions of amplicons)
$fragments = preg_split("/($start_pattern)/", $sequence,-1,PREG_SPLIT_DELIM_CAPTURE);
$maxfragments=sizeof($fragments);
$position=strlen($fragments[0]);
$mn=0;
for ($m=1;$m<$maxfragments; $m+=2){
$subfragment_to_maximum=substr($fragments[$m+1],0,$maxlength);
$fragments2 = preg_split("/($end_pattern)/", $subfragment_to_maximum,-1,PREG_SPLIT_DELIM_CAPTURE);
if (sizeof($fragments2)>1){
$lenfragment=strlen($fragments[$m].$fragments2[0].$fragments2[1]);
$results_array[$position]=$lenfragment;
}
$position+=strlen($fragments[$m])+strlen($fragments[$m+1]);
}
return($results_array);
}
// ####################
function RevComp($p2){
$p2=strrev($p2);
$p2=str_replace("A", "t", $p2);
$p2=str_replace("T", "a", $p2);
$p2=str_replace("G", "c", $p2);
$p2=str_replace("C", "g", $p2);
$p2 = strtoupper ($p2);
return $p2;
}
// ####################
function includeN($pattern) {
if (strlen($pattern)>2){
$new_pattern=".".substr($pattern,1);
$pos=1;
while ($pos
In silico PCR amplification
In silico PCR amplification
Source code