when I split it with a newline the data-lines also split up.

Instead of splitting on all newlines (as split would do by default) 

    my (@title) = split(/\n/,$output);

[download]

you could tell split to split into two parts only: 

    my ($title, $data) = split /\n/, $output, 2;

[download]

In this case, $data would hold all the remaining lines of sequence data.

That said, I'm not really sure why you want to split the record in the first place, if you then proceed to print out the parts with the same newline added in between them :)  I.e. 

    ...
    print ">".$title."\n".$data."\n";

[download]

would result in the same output as 

    print ">$output\n";

[download]

In reply to Re^7: Compare hash with arrays and print by almut
in thread Compare hash with arrays and print by ad23

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