Searching a sequence of bytes in a binary file in PHP?

First of all your $mysequence is not changing while search, so you can call hex2bin($mysequence) once and compare it with $seq directly.

As for doing it really faster, you can try read and search for string in large buffers. Larger buffer => faster search, but more memory needed. Fast code draft, how this should look like:

$mysequence = "4749524f";
$searchBytes = hex2bin($mysequence);
$crossing = 1 - length($searchBytes); // - (length - 1); see below
$buf = ''; $buflen = 10000;
$f = fopen($filename, "r") or die("Unable to open file!");
while(!feof($f)) 
{
    $seq .= fread($f, $buflen);
    if(strpos($seq, $searchBytes) === false) // strict comparation here. zero can be returned!
    {
        // keep last n-1 bytes, because they can be beginning of required sequence
        $seq = substr($seq, $crossing);
    }
    else
    {
        echo "found!";
        break;
    }
}
unset($seq); // no need to keep this in memory any more