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Mostly FASTA file contain NNN characters, which can be replace by random A T G C character with this perl script. It also print the FASTA sequence name, N's counts, nucleotide count and percentage details at command prompt/standard output.  

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...