@molecules = <MOL>;
map { chomp; $_ = quotemeta; } @molecules;

##</code><code>##

push my @molecules, quotemeta chomp while <MOL>;

##</code><code>##

$bigRegex = join '|', @molecules;

##</code><code>##

my $bigRegex;
($bigRegex .= join( '|', '\b'. $_ . '\b' ) ) for @molecules;

##</code><code>##

my $bigRegex;
$bigRegex = join '|', map { "\b$_\b" } sort { length $b <=> length $a } @molecules;

##</code><code>##

#!/usr/bin/perl -w
use strict;

open( MOL, "molecules" ) or die "ack! - $!";
push my @molecules, quotemeta chomp while <MOL>;
close MOL or warn "ack - $!";

my $bigRegex;
$bigRegex = join '|', 
    map { "\b$_\b" } 
    sort { length $b <=> length $a } @molecules;

open( LOCUS, "locus" ) or die "ack! - $!";
my @locus = <LOCUS>;
close LOCUS or die "ack! - $!";

for(@locus) 
{
    print if( scalar( split /\t/ ) >= 6 
        && /^([^\t]*\t)?($bigRegex)/ );
}