You clearly want to slurp the whole file
What if the file is hundreds of megs? Here's a little something I whipped up: 
use strict;
use warnings;

my $buf_size = 16_384;
open(my $big, shift) or die;
open(my $small, shift) or die;
my $search_string;
{
        local $/;
        $search_string = <$small>;
}
my $buffer = "";
my $pos = 0;
while(sysread($big, $buffer, $buf_size, length($buffer) ) ) {
   if ( (my $index = index($buffer, $search_string)) != -1)  {
      print "FOUND! found the search string at position ", $pos + $ind
+ex;
      exit;
   }
   $buffer = substr($buffer, int(length($buffer)/2));
   $pos += length($buffer);
}

print "search string not found";

[download]

I'll grant that this also falls prey to the same problem that your has if the smaller file is itself large, but I think that in general this scales much better.

thor

Feel the white light, the light within
Be your own disciple, fan the sparks of will
For all of us waiting, your kingdom will come

f

In reply to Re^2: searching for a binary string in a binary file by thor
in thread searching for a binary string in a binary file by rochlin

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