EDIT: (More of a complete 180, really): I somehow completely missed the fact you already asked the exact same question in Re^2: Reverse Complement and had a lengthy exchange with AnomylousMonk, who was very helpful.

I actually used the exact same structure (and even used the exact same error messages!) that you provided in the original post. Did you write that code yourself? Anyway, I also gave a direct example of how to run the script. Assuming you saved the script as 1041523.pl (an odd name, to be sure—feel free to choose a better one), type the following:

perl 1041523.pl GGGGaaaaaaaatttatatat atatataaattttttttcccc

Of course, substitute any two sequences for the two shown here.

In reply to Re^3: Reverse Complement by rjt
in thread Reverse Complement by stamp1982

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