I believe Fletch is right about the NULLs. The "concatentation" in your error message comes from interpolating the results into the string in this line:

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

One easy way to turn undef's into reasonable values is this idiom:

   $giName ||= " ";
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I don't see a lot to optimize, but here are my suggestions:

   # 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->fetchro
+w_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";
    }
[download]

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