A pair of substitutions with a regular expression anchored to the start and end of the string will help. 
$dna = "NNNNATCGNNNTCGANNN";
$dna =~ s/^[N]+//;
$dna =~ s/[N]+$//;
print "$dna\n"
__END__
ATCGNNNTCGA

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

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