function Neighbors($Pattern, $d)
{
/*
* Neighbors(Pattern, d)
if d = 0
return {Pattern}
if |Pattern| = 1
return {A, C, G, T}
Neighborhood ← an empty set
SuffixNeighbors ← Neighbors(Suffix(Pattern), d)
for each string Text from SuffixNeighbors
if HammingDistance(Suffix(Pattern), Text) < d
for each nucleotide x
add x • Text to Neighborhood
else
add FirstSymbol(Pattern) • Text to Neighborhood
return Neighborhood
*/
if ($d == 0) {
return $Pattern;
}
$nucleotides = array('A' => 'A', 'C' => 'C', 'G' => 'G', 'T' => 'T');
if (strlen($Pattern) == 1) {
return $nucleotides;
}
$Neighborhood = array();
$Suffix = substr($Pattern, 1);
$Prefix = substr($Pattern, 0, 1);
$SuffixNeighbors = Neighbors($Suffix, $d);
foreach ($SuffixNeighbors as $Text) {
if (HammingDistance($Suffix, $Text) < $d) {
foreach ($nucleotides as $x) {
$Neighborhood[] = $x . $Text;
}
} else {
$Neighborhood[] = $Prefix . $Text;
}
}
return $Neighborhood;
}
<?php
require __DIR__ . '/../../_common.php';
echo HammingDistance('CTACAGCAATACGATCATATGCGGATCCGCAGTGGCCGGTAGACACACGT', 'CTACCCCGCTGCTCAATGACCGGGACTAAAGAGGCGAAGATTATGGTGTG');