function MotifEnumeration($dna_kmers, $k, $d)
{
/*
* Patterns ← an empty set
for each k-mer Pattern in Dna
for each k-mer Pattern’ differing from Pattern by at most d mismatches
if Pattern' appears in each string from Dna with at most d mismatches
add Pattern' to Patterns
remove duplicates from Patterns
return Patterns
*/
$Patterns = array();
foreach ($dna_kmers as $Pattern) {
$kmers_prime = GenerateAllKMers($Pattern, $k);
foreach ($kmers_prime as $Pattern_prime_x) {
//ddd($Pattern_prime_x, FALSE);
$Neighbours = Neighbors($Pattern_prime_x, $d);
foreach ($Neighbours as $Pattern_prime) {
//ddd($Neighbours);
$score = 0;
foreach ($dna_kmers as $Pattern_for_count) {
if (ApproximatePatternCount($Pattern_for_count, $Pattern_prime, $d) > 0) {
$score++;
}
}
if ($score == count($dna_kmers)) {
$Patterns[] = $Pattern_prime;
}
}
}
}
return array_unique($Patterns);
}
<?php
require __DIR__ . '/../../_common.php';
echo ApproximatePatternCount('CTGTACCCGTAGAGCCCATTAACATCTGCATGAGCGTTCTGGGGCCTCTTAACGCGATTGTGAACTAAAATACTAATATATGATGTCAACGTTGGGGAAACCCACCTAATGTCAACACCTATGCTACACGACGCTACGAAAGTGTGTGCCCGTACCGGAAGGCACGGATCTGTGCGTCCCCATTGACCACAGTTTAGATCGCCGAACTGCACTATACGCTTTCGATTAGACAACCGATCGCACCAGGCCTGTAGTATACCAAAAGTGTTACACCGCGATACCGAGCAGGACAATGATTATCCGAATGCATGTCCCGGGGCGATAGTTTTTTAGACAGACCGCCTTTCCTCTACTCATGCATTGGGG', 'CATGTC', 3);