BOL

You can use a s/// regex like this:

my $str = "This is my string";
my $find = "string";
my $replace = "strings";
$find = quotemeta $find; # escape regex metachars if present

##The quotemeta lets you find strings that contain regex meta characters and the /g at the end of the s/// does all occurances.

$str =~ s/$find/$replace/g;

print $str;

Thanks

Thats true .. by using  s/// regex will remove the N's, but if you need to replace them with randomly generated nucleotide sequence then use this script http://bioinformaticsonline.com/file/view/5307/clean-the-fasta-file which will clean the N's with random A T G C characters.