[Bioclusters] Versions of Blast that run on a cluster?

[Malay]

Joe Landman wrote:
> Daniel.G.Roberts at aventis.com wrote:
> 
>> Hello All
>> Can anyone point me to example/FAQ resources on BLAST implemented on a 
>> Linux Cluster?
>>
> 

It depends on your blast job. There are two ways to accelerate:

If you have thousand of sequences then the best way is to have a 
dedicated NFS server running of gigabit LAN and each node with ample 
amount of RAM. Use NCBI blast through a good job scheduler like SGE and 
throw each sequences as a separte blast job with BLAST database shared 
over Gigabit LAN. From day to day experience I can say a routine NFS 
mount can use around ~250 sequences at a time.

If you have very few sequences and want to just run a single job as fast 
as possible, the best way is to split the database. mpiBLAST is best 
known for that or you can even use your own custom script. Remember that 
it will screw up the BLAST statistics.

-Malay
mbasu(at)ncbi.nlm.nih.gov