It looks it will work, but only insofar you have only one long line in your file. If your file comes with more than one line, you're in trouble. I would use a loop or some other mechanism to make sure it will still work fine the day I get two or more lines. Below, I localized $/ (the input record separator) so that the whole file will be slurped into the scalar.

As a side note, there are some commonly agreed best practices in the Perl community. Among them:

• use the use warnings; pragma rather than the -w flag
• Use lexical filehandles rather than bareword filehandles
• Use the three-argument syntax for the open function

Putting all this together, this a possible (untested) rewrite of your script:

#!/usr/bin/perl

use strict;
use warnings;

my $infile = shift;

open my $INPUT_FILE, "<", $infile" or die "can't open $infile: $!";

local $/; # the whole file will be slurped, even if it has several lin
+es
my $dna = <$INPUT_FILE>;         
if ( $dna  =~ m/[^actg\s]/i ) {
    print "File contains something besides actg sequence.\n";
} else {
    print "good!\n";
}            
close $INPUT_FILE;
[download]