I think that in this case, you don't need to worry about signal handlers (not for the reasons you think anyway). Your script does 2 things:

1. Maintain a connection to a remote database
2. Call a remote BLAST server

I don't have a clue about what a BLAST server is, but I imagine it does something interesting with a DNA sequence.

To detect problems with the database, you can reconnect for every query so that when the database is down, you get an error message, or use a permanent connection and create a timeout handler using signals and the alarm system call.

You'll have to do something similar with the requests to the BLAST server. I don't know what a call to the BLAST server looks like, but I assume something like the database query can be done.

Using the temp file for intermediate results is a wise thing, because when a connection to one of the servers is down, you can detect it and wait for it to come back up (using sleep for example), possibly notify you, and go on its merry way. This way, you can do all error handling within the script and there's no need to monitor external processes.

Arjen