print FILE ">$giName $gssName $definition\n$sequence";

##</code><code>##

   $giName ||= " ";

##</code><code>##

   # makes array interpolate with newlines
   local $" = "\n";
   # Pull my variable declarations outside the inner loop.
   my ($giName, $gssName, $definition, $sequence, @seq);
   while (($giName, $gssName, $definition, $sequence) = $sth2->fetchrow_array )
   {
      $sequence = uc( $sequence );

      # If I'm right about your data, you just want to
      # turn the whitespace into newlines.
      # The following should be faster.
      @seq = split /\s+/,$sequence;

      # For any fields that can be null:
      $giName ||= " ";

      # Less interpolation will be faster, but we need it
      # for the array.
      print FILE ">",$giName," ",$gssName," ",$definition,"\n","@seq","\n";
    }