My apologies for being so slow. At the moment this is what I have. 
perl -wMstrict -l  your_file.pl  GGGGaaaaaaCatttatatat  atatataaattttt
+ATtcccc

die "Please enter two sequences as arguments on the command line\n"
    unless @ARGV == 2;

my ($orig, $comp) = map { uc } @ARGV;
die "Please enter only ATCG sequences\n" if grep { /[^ATCG]/ } $orig, 
+$comp;

die "Sorry, the two sequences you have just entered are of different l
+engths."
  . "\nPlease try again on the command line.\n" 
    if length $orig != length $comp;

# $comp will transform back to $orig iff it is the reverse complement
$comp =~ y/ATCG/TAGC/;

if ($orig eq reverse $comp) {
    print "Yes, the two sequences are reverse-complement of each other
+.\n";
    exit;
} else {
    die "Unfortunately, the two sequences are not reverse-complement.\
+n";
}

[download]

comments I get are : unquoted strings may clash with future reserved words and compilation error and syntax error at wMstrict -l

In reply to Re^4: Reverse Complement by stamp1982
in thread Reverse Complement by stamp1982

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