[BiO BB] custom blast server

Joel Dudley Joel.Dudley at DevelopOnline.com
Thu Dec 6 11:21:42 EST 2001

Well I have no problems using the NCBI BLAST, but does it run as a HTTP
service out of the box? or do I need to wrap it on some server code? my main
problem is that I am not interested in returning high scoring sequences,
rather I need to get another value associateed to the high scoring sequences
and return a file. That is where arrangement is custom.

- Joel

Honestly, no.  From the best I can figure out, you have an application
and a BLAST server that are running on separate machines across the
internet.  You want the BLAST server to be able to handle multiple
requests concurrently, and you have a relational database of sequences
that you want to BLAST against.

The standard way to do this is to run BLAST over HTTP, and fork an
instance of the executable for every run.  You'll get less performance
than a persistant multi-threaded one, but I don't think that's how
NCBI BLAST is written.  And anyway, the bottleneck is going to be the
database searches, not the process forking.

I think Iddo asked a good question, and I'm also wondering about the
requirement to be run off the SQL database.  I'm not sure what that
has to do with threading and XML RPC.


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