[Bioclusters] mpiblast

[Joe Landman]

Chuming Chen wrote:
> Hi all,
> 
> Does the query size of mpiblast effect the total performance?

Each blast operation is a function of the length of the query sequence, 
as well as the length of the database.  Usually people talk about the 
average query length as well as the size of the query.

> 
> It took about 17 seconds per sequence when I run 721  sequences  (542K) 
> against 22G database.

You have that here:  542k bp/721 seq gives you a rough average.

> But when I run 88532 sequences (47M) against the same database, it  took 
> about 1 minute.

Same thing here.  The two may have very different sequence length mixes.

> 
> Can the performance be improved if the query sequence is in a  
> relatively smaller size?

Depends upon the algorithm being used.

> 
> Thank you for your kind comments and suggestions.
> 
> Chuming Chen
> 
> 
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