[BioDarwin] BLASTN benchmarks

[Corentin Cras-Méneur]

At 10:42 -0500 02/09/2003, David Adelson wrote:
>
>Corentin,

	Dave,


>Feel free to download the query sequences and run them with WU-BLAST.


I might try it.

>   We tried WU-BLAST on all of our machines but ran into problems 
>getting it to run on the Xserves due to the 2GB memory limitation of 
>that architecture.

I see. I never encountered this situation before.

>   We could get searches to run against Chromosome 21 but not against 
>any longer sequences.   As  we would have had to break up longer 
>database sequences we decided not to pursue the exercise, as the 
>time spent fiddling around with sequence databases argued against 
>any other gains in efficiency. NCBI (AG) BLAST is easy to set up and 
>use and no special alterations of the databases is required.  For 
>smaller databases or rather databases comprised of shorter sequences 
>WU-BLAST might be a useful option, but it does not do what we need 
>it to do without considerable fiddling around.


It is true that I am mostly using BLAST on databases with rather 
small (but numerous) sequences.


		Corentin