N
$seqb=preg_replace("/X/", "N", $seqb); // substitute X -> N
// LIMIT SEQUENCE LENGTH TO LIMIT MEMORY USAGE
// THIS SCRIPT CREATES A BIG ARRAY THAT REQUIRES A HUGE AMOUNT OF MEMORY
// DO NOT USED SEQUENCES LONGER THAN 700 BASES EACH (1400 BASES FOR BOTH SEQUENCES)
// IN THIS DEMO, THE LIMIT HAS BEEN SET UP IN 300 BASES
$limit=300;
if ((strlen($seqa)+strlen($seqb))>$limit){die ("Error: The maximum length of code accepted for both sequences is $limit nucleotides");}
// CHECK WHETHER THEY ARE DNA OR PROTEIN, AND ALIGN SEQUENCES
if ((substr_count($seqa,"A")+substr_count($seqa,"C")+substr_count($seqa,"G")+substr_count($seqa,"T"))>(strlen($seqa)/2)){
// if A+C+G+T is at least half of the sequence, it is a DNA
$alignment=align_DNA($seqa,$seqb);
}else{
// else is protein
$alignment=align_proteins($seqa,$seqb);
}
// EXTRACT DATA FROM ALIGNMENT
$align_seqa=$alignment["seqa"];
$align_seqb=$alignment["seqb"];
// COMPARE ALIGNMENTS
$compare=compare_alignment($align_seqa,$align_seqb);
// PRINT RESULTS
print "