Saturday, 21 November 2015

Is this the shortest abstract ever?

I’m currently writing a new program as part of a comparative genome analysis, which has the working title of “Snapper”. Unusually (but not uniquely) for me, this is not an acronym, but is instead a simple contraction of “SNP Mapper”.

Before doing too much, it is always wise to check for existing tools with the same name, especially if they might do similar things. A quick Google search for “Snapper bioinformatics” threw up this paper:

  • Kolesov G, Mewes HW & Frishman D (2002). SNAPper: gene order predicts gene function. Bioinformatics 18(7):1017-9.

The abstract:

SNAPper is a network service for predicting gene function based on the conservation of gene order.

The SNAPper server is available at SNAPper-based functional predictions will soon be offered as part of the PEDANT genome analysis server

I know that Bioinformatics application notes are pretty concise - the idea is that the described software has the documentation you need - but that has to be one of the shortest abstracts that I have ever seen!

SNAPper itself is not an acronym, although the SNAP part is: Similarity Neighbourhood APproach. For such a common acronym as “SNAP”, that one needs some work, I think.

PEDANT, on the other hand, is a full ORCA-worthy acronym: Protein Extraction, Description and ANalysis Tool. It reminds me a bit of a defunct classic of my own, PIRATE: Protein Identification, References, Annotation and Tissue Extraction (or something like that, lost in the mists of time) that was basically just a parser for Uniprot entries that tabulated certain data, after I discovered that a PhD student in the department had spent several days copying and pasting data from Uniprot into Excel. Happy days!

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