Hi,

Actually, I think you could use two regexs here:

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

[download]

If this works for you, we could even optimize and consolidate this code a bit. I don't know where $s comes from, but I assume the lenght isn't changing any.

my $length = length $s; # Pull this out of the loop for eff.
my $sequence = $seq{$k};

while ($sequence =~ /([QGYN]{3,6})/g) {
     my $seq = $1;
     my $pos = $-[0] - $length; # @- holds the positions on the last m
+atch
     next if $seq =~ /(.)\1\1/;
     print "\n$k $seq begins at position $pos\n";
}

[download]

update: that was supposed to be print, not printf

Note that this is untested...

Ted Young

($$<<$$=>$$<=>$$<=$$>>$$) always returns 1. :-)

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

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