#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

my ($in_file, $out_file) = qw{temp_in.txt temp_out.txt};

open my $in_fh, '<', $in_file;
open my $out_fh, '>', $out_file;

my @protein;

while (<$in_fh>) {
    chomp;

    if (/^>(.*)$/) {
        print_reverse_decoy(\@protein, $out_fh);
        print $out_fh ">Reverse Decoy $1\n";
    }
    else {
        push @protein, $_;
    }
}

print_reverse_decoy(\@protein, $out_fh);

sub print_reverse_decoy {
    my ($protein, $out_fh) = @_; 
    print $out_fh "$_\n" for map { scalar reverse split '' } reverse @$protein;
    @$protein = (); 
    return;
}

##</code><code>##

$ cat temp_in.txt
>Sequence 1
ABCDEFG
HIJKLMN
>Sequence 2
OPQRST
UVWXYZ
>Sequence N
1234567890
!@#$%^&*()

##</code><code>##

$ cat temp_out.txt
>Reverse Decoy Sequence 1
NMLKJIH
GFEDCBA
>Reverse Decoy Sequence 2
ZYXWVU
TSRQPO
>Reverse Decoy Sequence N
)(*&^%$#@!
0987654321