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#!/usr/bin/env perl

...
    @$protein = (); 
    return;
}

$ cat temp_in.txt
>Sequence 1
...
>Sequence N
1234567890
!@#$%^&*()

$ cat temp_out.txt
>Reverse Decoy Sequence 1
...
>Reverse Decoy Sequence N
)(*&^%$#@!
0987654321