Here's another shorter regex (although it's not doing any substitution):

...
print $fh ">$description\n";
print $fh "$_\n" foreach ($seq =~ /.{1,50}/g);
...
[download]

The fastest way I've found of dumping a FASTA sequence (with very large sequences, anyways), is with substr:

...
print $fh ">$description\n";
print $fh substr($seq,0,50,'') . "\n" while ($seq);
...
[download]

The thing to watch here is that it's destructive - $seq will be empty when it finishes.

- robsv