No Mike, you're not blind nor stupid. The ability to use blastcl3 with
DBWatcher is a recent modification and it is not mentioned in the doc
yet, sorry. The Linux executables were built some time ago by Ashok
Aiyar and do not implement this modification.
You can get the sources for the Blastcl3 DBWatcher version at:
I still haven't got any Linux binaries, so you'll have to compile the
whole thing. Sorry about that.
This modified version is not an actual client of the NCBI Blast server
(as the original was) but uses directly the "blastcl3" executable
available from the NCBI. Therefore, you don't need the blastcl3
libraries. You don't even need the NCBI toolkit if you don't want to
BTW, it is also able to run "blastall" for local Blast2 searches...
I hope this helps,
Do not hesitate to contact me if you have any problem.