[Bioclusters] BLAST job time estimates

Micha Bayer bioclusters@bioinformatics.org
01 Jun 2004 11:57:32 +0100

Hi all,

has anyone got a method for calculating predicted estimates for the time
it takes to run BLAST jobs using NCBI BLAST and also mpiBLAST? 

I am setting up a job submission system on our local grid and one of our
clusters requires you to provide an estimate of the predicted runtime so
that the job can be positioned accordingly in the queue.

I just need a formula to work out the time it takes to run a single job
on a single processor.

A formula would presumably take into account things like the length and
number of the input queries, the size and makeup of the target database
(i.e. number and length of sequences contained in this), the
similarities between the query and the target sequences and local
hardware parameters (processors, memory, local network speeds etc).

There may be stuff about this in the literature but I haven't seen any -
if anyone knows of references that would also be greatly appreciated.


Dr Micha M Bayer
Grid Developer, BRIDGES Project
National e-Science Centre, Glasgow Hub
246c Kelvin Building
University of Glasgow
Glasgow G12 8QQ
Scotland, UK
Email: michab@dcs.gla.ac.uk
Project home page: http://www.brc.dcs.gla.ac.uk/projects/bridges/
Personal Homepage: http://www.brc.dcs.gla.ac.uk/~michab/
Tel.: +44 (0)141 330 2958