... in the end I have to manually enter each nucleotide, am I understanding this right? In other words I can't be lazy and store several DNA files I downloaded online into arrays and then operate on them. For each of my array I have to manually type the nucleotide sequences in myself or copy+paste them in
You have to realize that when you read a file with | with a sequence of statements like
$DNA3file = 'testDNA3';
open(DNA3handle, $DNA3file);
@DNA3 = <DNA3handle>;
the @DNA3 array ends up with all the lines of the file, and each line is a string that looks like "ATCCATGC\n" (note the newline that will be at the end of (almost) every line).
If you have the lines of the file as strings, you | your program can operate on them as strings, break them up into arrays and operate on them, etc., as appropriate for your application. Your choice.
Give a man a fish: <%-{-{-{-<