Build that programmatically. 
my $regex = '(([QGYN])';
$regex .= '((?!\\' . $_ . ')[QGYN]|\\' . $_. '(?!\\${_}))' for 2 .. 3;
$regex .= '(?:((?!\\' . $_ . ')[QGYN]|\\' . $_ . '(?!\\' . $_ . '))' f
+or 4 .. 5;
$regex .= '[QGYN]?)?)?)';
$regex = qr/$regex/;

while ($seq{$k} =~ /$regex/g)
{
    print "\n$k";
    print $1." begins at position ", (pos($seq{$k})-length($s)) , "\n"
+;
}

[download]

Now, I have no idea what all that does, but it's easily broken apart. :-)

Being right, does not endow the right to be rude; politeness costs nothing.
Being unknowing, is not the same as being stupid.
Expressing a contrary opinion, whether to the individual or the group, is more often a sign of deeper thought than of cantankerous belligerence.
Do not mistake your goals as the only goals; your opinion as the only opinion; your confidence as correctness. Saying you know better is not the same as explaining you know better.

In reply to Re^2: Perl regular expression for amino acid sequence by dragonchild
in thread Perl regular expression for amino acid sequence by seaver

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.