mpiBLASTx

[cement_head]

Hello,

This might be the wrong sub-forum, but how long should 55,000 cDNAs take to blastx using mpiBLAST? We are using 16 nodes.

Thanks,
Andor

[SES]

It depends on other factors besides the number of sequences, such as the length of the database and the computational resources, so it is probably not possible to make a sensible prediction. 55k sequences is not a large number by any means and you may want to try using multiple CPUs on a single node vs. multiple nodes to see if using mpiBLAST offers a real advantage.

[GenoMax]

Is that a preparatory question or are you already running this and want to know how long it may take.

It may be easier to break your search in multiple files and run them in parallel using standard blastx as independent jobs on your cluster. mpiBlast is probably using an older implementation of blast, unless you are planning to use the commercial version (abokia blast).