Hello,
Sorry for this late contribution but we have had a hard time fixing
some problems with our web server.
As Harry mentionned, the NCBI discontinued their Blast 1.4 services.
The blastcl2 libraries from the NCBI toolkit, which I used to write
the client version of DBWatcher, are not supported anymore. From what
I could see, the blastcl3 libraries are quite different from blastcl2.
I'm afraid it might take much time and energy to implement the new
libraries in DBWatcher. Actually, I'm not quite sure I want to spend
that energy as I have more general projects for DBWatcher including,
remote blast searches among other facilities. (more on this later...
maybe... )
However, I've recently worked on a quick fix to run local gapped Blast
from DBWatcher and it works alright. The good news for those who don't
have local databases is that the standalone blastcl3 client, available
from the NCBI ftp server, works exactly the same as the blastall local
program. I therefore modified my local gapped Blast fix to make it
work with the blastcl3 client program as well.
It is (still?) not able to tell whether the database has been updated
and runs the remote Blast search every time, but at least it works OK
and you may carry on with your DBWatcher jobs. But, please, keep in
mind that this is only a temporary hack.
If you are interested to get the DBWatcher_BlastCL3 version, you may
contact me at plewniak at igbmc.u-strasbg.fr
Best regards,
Fred
