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mpiBlast is a freely available, opensource, parallel implementation of NCBI Blast. mpiBlast takes advantage of shared parallel computign resources, i.e. a cluster this gives it access to more avaliable resources unlike NCBI blast which only can take advantage of shared-memory multi-processors(SMP's).

More information is available here.

Environment Setup

Make a directory to contain the FASTA database that will be fragmented. Download the database and decompress it.

razor-l1:jokinsey:~$ mkdir db
razor-l1:jokinsey:~$ cd db
razor-l1:jokinsey:~/db$ wget
razor-l1:jokinsey:~/db$ gunzip mito.nt.gz

Create a $HOME/.nbirc file with these values. The shared path tells mpiBlast where to access the FASTA database.


Format the database for parallel use, by fragmenting the database for each processor. We will be using a node with 12 processors so we will include the option - -nfrags=12.

mpiblast.1505249812.txt.gz · Last modified: 2017/09/12 20:56 by jokinsey