This solution is actually fairly wrong since it first attempts to take from the front instead of trying to shorten the match. Of course, this is if QGNNNG would be considered series of two valid amino acids, being QGN and NNG.

my $cur;
while ($seq{$k} =~ /([QGYN]{3,6})/g) {
   $cur = $1;
   pos($seq{$k}) -= length($cur) - 1 and next if $cur =~ /(.)\1\1/;
   print "\n$k";
   print $cur." begins at position ", (pos($seq{$k})-length($s)) , "\n
+";
}

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In reply to Re^3: Perl regular expression for amino acid sequence by !1
in thread Perl regular expression for amino acid sequence by seaver

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