With reference to your regex, I always find it a bit sadomasochistic to use regular expression meta characters to delimit a regular expression, it does kind of muddy the waters.

Also, your regex is quite inefficient, as perl has jump through hoops to save the value captured in the parentheses. It's quicker to "top and tail" the string over two lines. Three times quicker in fact... 

#!/perl -w 
use strict;
use Benchmark;

timethese(200000, {
    'single' => sub {
                        my $dna = "NNNNATCGNNNTCGANNN";
                        $dna =~ s/^N*(.*?)N*$/$1/;
                    },
    'twin'   => sub {
                        my $dna = "NNNNATCGNNNTCGANNN";
                        $dna =~ s/^N*//;
                        $dna =~ s/N*$//;
                    },
});


__OUTPUT__
Benchmark: timing 200000 iterations of single, twin...
    single:  3 wallclock secs ( 2.95 usr +  0.00 sys =  2.95 CPU) @ 67
+704.81/s (n=200000)
      twin:  1 wallclock secs ( 0.83 usr +  0.00 sys =  0.83 CPU) @ 24
+0963.86/s (n=200000)

[download]
---
my name's not Keith, and I'm not reasonable.

In reply to Re^2: Removing Flanking "N"s in a DNA String by reasonablekeith
in thread Removing Flanking "N"s in a DNA String by monkfan

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