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  1. or download this
    my %acgt; @acgt{ qw[ a c g t ] } = 0 .. 3;

...
        for 0 .. 15;
    return unpack 'N',  $bits;
}
  2. or download this
    my $lookup = '';
while( <SMALLFILE> ) {
    chomp;
    vec( $lookup, encode( $_), 1 ) = 1;
}
  3. or download this
    while( <BIGFILE> ) {
    chomp;
    print if vec( $lookup, encode( $_ ), 1 );
}