Friday, 4 July 2014

WImpiBLAST - Web Interface for mpiBLAST

Although BLAST is a deserved ORCAcronym in its own right, it is also notable for the number of spin-offs and add-ons that it has produced. One such program is mpiBLAST, an open-source parallelisation of BLAST. This is turn has spawned WImpiBLAST - Web Interface for mpiBLAST. I’m not sure if WImpiBLAST deserves a new “anti hoc” class of acronym, as parallelisation of BLAST on a supercomputer is anything but wimpy. Ad hoc will do for now.

You can find out more at RNA-Seq Blog or the paper:

BLAST - Basic Local Alignment Search Tool

If there is one bioinformatics program that every biologist has heard of, it is BLAST: Basic Local Alignment Search Tool. In fact, BLAST is so popular and famous that many people probably don’t know that it is an acronym nor what it stands for; “to BLAST” has become a verb in common use. For non-biologists, BLAST is a homology search tool, which means that it finds similarities between biological (nucleotide or protein) sequences, and biologists will frequently “BLAST a sequence against a database” to find similar sequences.

The original BLAST algorithm is pretty old, which is part of the reason for its widespread fame. I’m not sure of the stats but the original Altschul et al. (1990) paper must be one of the most cited of all time.

Certainly a worth addition to ORCA. (Although the main motivation for adding it is for the next post!) Given that BLAST works by fragmenting the query sequence into pieces for the initial search, I think that it rates at least as a post hoc.