Buy one bogus bioinformatics acronym, get one free!

New in the journal Bioinformatics:

So the software is called AdvISER-M-PYRO and this is (presumably) derived from Amplicon identification using SparsE representation of multiplex PYROsequencing. However, I don't understand why 'S', 'E', and 'PYRO' get capitalized but not the 'I' of 'identification' or the 'M' of 'multiplex'? Also, I like how they sneak in two letters ('d' and 'v') that don't occur in the name of the software (at least not before the 'I' of 'identification').

This paper is a 2-for-1 type of deal, because if you read a bit more of the abstract you will see:

In parallel, the nucleotide dispensation order was improved by developing the SENATOR (‘SElecting the Nucleotide dispensATion Order’) algorithm.

This second bogus acronym also lacks some clarity. Is the 'R' of 'SENATOR' derived from the first or second 'r' of 'the word 'Order'???

Time for a new JABBA award for Just Another Bogus Bioinformatics Acronym

From the journal Bioinformatics, we have:

The bogus nature of this acronym is quickly revealed from the very first line of the abstract:

We introduce PEPPER (Protein complex Expansion using Protein–Protein intERactions)

Winning a JABBA award is one thing, but you get bonus points if you decide to use the same name as a completely different bioinformatics tool (something that is, sadly,  becoming more common). So if you run a Google search for pepper bioinformatics, you may also come across a molecular visualizer called PeppeR.

Turkey bioinformatics by the numbers

  • 109,700,700 - mean divergence time (in years) between turkeys (Meleagris gallopavo) and turkey vultures (Cathartes aura)
  • 101,849 - number of turkey nucleotide sequences in GenBank
  • 3,597 - number of selenoproteins in UniProt which allow for the possibility of generating a peptide called ‘TURKEY’ (the IUPAC code for selenocysteine is U)[1]
  • 1 - number of published turkey genomes
  • 0 - number of bioinformatics tools that have tried using ‘turkey’ as part of a bogus acronym in their name[2]

  1. I can’t find any such peptide when using the UniProt BLAST server though :-(  ↩

  2. And let's try to keep it that way! ↩

More mixed-case madness in the name of a bioinformatics tool

From the latest issue of Bioinformatics we have:

According to the abstract, the 'SUB' comes from subcellular, the 'A' comes from Arabidopsis, and the 'con' comes from 'consensus'. So why isn't it SUBACON? Maybe because people might then read it as 'sue bacon'?

It's not clear to me if this is meant to be pronounced 'soo-ba-con' or 'sub-ay-con'. The abstract then goes on to mention something called the ASURE portal (pronounced 'azure' or 'ay-sure'???), where ASURE = Arabidopsis SUbproteome REference.. If this was following the same rules as SUBAcon, shouldn't this be called ASUre (or even ASUBre)?