while (<DATA>) {
    chomp;
    my ($head, $seq) = split / /;
[download]

That would be better as:

while ( <DATA> ) {
    my ($head, $seq ) = split;
[download]

my @file_ends = qw{./ .fasta};
...
                open my $fh, q{>>}, join($ko, @file_ends);
[download]

With three argument open you don't need to prepend the file name with "./" and you should always verify that the file successfully opened before trying to use a possibly invalid filehandle:

my file_end = '.fasta';
...
                open my $fh, '>>', "$ko$file_end" or die "Cannot open 
+'$ko$file_end' because: $!";
[download]