my $longuest_sig_len = ...;

my $block_size = 4096;
$block_size = int(($longuest_sig_len + 1023) / 1024)
   if $block_size < $longuest_sig_len;

local $/ = \$block_size;
my $block = '';
while (<$fh>) {
   $block = substr($block, -($longuest_sig_len-1)) . $_;

   ... search for signature in $block ...
}