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:

• Sharma P & Mantri SS (2014) “WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing.” PLoS ONE 9(6): e101144.

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.

• Altschul S, Gish W, Miller W, Myers E & Lipman D (1990). “Basic local alignment search tool”. Journal of Molecular Biology 215 (3): 403–410.

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.

MFSPSSMpred - Masked, Filtered and Smoothed Position-Specific Scoring Matrix-based predictor

Today’s post is a bit odd, as it is an anti-ORCA acronym. There is a reason why contrived acronyms exist, and I think that MFSPSSMpred is a prime example. The acronym itself is almost informative, although it fails to identify what it is trying to predict. (Short molecular recognition features in this case.) Still, imagine yourself in a lab meeting, trying to tell your supervisor which prediction tool you were using from memory!

MFSPSSMpred does have one thing going for it, though, and that’s Google-friendliness. Providing you spell it right, that is!

P.S. Whilst Googling MFSPSSMpred, I discovered that OCTAGON-winning Keith Bradnam got there first and MFSPSSMpred is a JABBA Award winner!

ARENA - Australian Renewable ENergy Agency

ARENA is the Australian Renewable Energy Agency,

an independent agency established by the Australian Government on 1 July 2012. We have two objectives: to improve the competitiveness of renewable energy technologies, and to increase the supply of renewable energy in Australia.

Unfortunately, ARENA was one of the losers from the recent Australian budget and might not be around much longer.

HOTAIR - HOX Transcript Antisense RNA

According to Wikipedia:

HOTAIR (for HOX antisense intergenic RNA) is a human gene located on chromosome 12. It is the first example of an RNA expressed on one chromosome that has been found to influence transcription on another chromosome.

However, Wikipedia itself cites Genecards, which has a slightly different metanym expansion (without any missing letters) for HOTAIR: HOX Transcript Antisense RNA. Either way, a very interesting gene and, though ad hoc intranym, certainly contrived enough for ORCA!

(HOTAIR possibly needs a new ORCA classification because both “metanym” sub-acronyms - HOX (Homeobox) and RNA (Ribonucleic acid) are themselves “itranyms”, as is HOTAIR.)

MODULUS - Methods Of Determining and Understanding Light elements from Unequivocal Stable isotope compositions

Another one from Rosetta, MODULUS - Methods Of Determining and Understanding Light elements from Unequivocal Stable isotope compositions - is described in Cosmos as part of the PTOLEMY instrumentation "to understand the geochemistry of light elements, such as hydrogen, carbon, nitrogen and oxygen".

That’s a lot of words and definitely an ORCA level of commitment to contrive a word out of it, even if they were not able to use them all!

miRCat - miRNA Categoriser

I am currently writing some lectures on RNA biology and came across the charmingly named miRCat: miRNA Categoriser.

This is a meta-acronym, with miRNA being short for microRNA (often abbreviated further to "miR" and pronounced “meer”, hence the logo) and RNA itself an acronym for Ribonucleic Acid).

miRCat is a tool to identify miRNAs in high-throughput small RNA sequence data… miRCat takes a FASTA file of small RNA reads as input and will map them to a reference genome… The tool then looks at genomic hit distribution patterns and secondary structure of genomic regions corresponding to sRNA hits and will predict miRNAs and their precursor structures.

Given the homophonic aspect of the acronym, I reckon this counts as pre hoc. As far as I am aware, “Categoriser” is not even a real (English) word, so this is definitely acronym contrivance worth of ORCA.