my ($file1, $file2) = qw(file1 file2);
open INDAT,  "<", $file1 or die "Cannot open ($file1) for reading: $!"; 
open INCOMP, "<", $file2 or die "Cannot open ($file2) for reading: $!";

while (defined (my $line = <INDAT>)) {
    chomp $line; # remove newline
    my @array = split /\t/, $line;

    while (defined (my $line = <INCOMP>)) {
        chomp $line;
        my @probes = split /\t/, $line;

        # using \Q and \E to avoid having regex meta character problems
        # see "perldoc perlre"
        if ($array[0] =~ /\Q$probes[1]\E/i) {
            print "Found $probes[1]\n";
        }
    }
}
close INCOMP;
close INDAT;