Normally, I introduce the name of the JABBA-award-worthy acronym before I show you the full name of the offending piece of software. But this time, let's play a little game. Here is the title of a recent article from the journal Bioinformatics, only I have removed the software acromym and the tell-tale capitalization from the name:

small molecule activity scanner web service based

So now you know the name, have a guess at what the acronym/initalism is. I feel confident that no-one will guess the answer. You'll have to scroll down for the reveal…

Okay, here it is:

SEABED: Small molEcule activity scanner weB servicE baseD

Note that:

Only the 'S' is clearly derived from the initial letter of a word
The 'A' is left ambiguously unexplained in the capitalization (as presented in the journal title). One might presume that it comes from 'Activity' but I wouldn't rule out 'scAnner'.
However you derive the letters in SEABED, one (or more) words don't contribute to the acronym at all.

All of which makes SEABED a worthy recipient of a JABBA award. The only saving grace is that a Google search for seabed bioinformatics finds the paper as the top hit.

One downside to this tool is that the SEABED webserver (http://www.bsc.es/SEABED) doesn't seem to working at all at the moment.