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Posts Tagged ‘bioinformatics’

Plega sp. (Mantispidae)

Who was the source of Monday’s DNA? As many of you discerned from the online Genbank database, the sequence came from Plega dactylota, a Neuropteran insect in the family Mantispidae.

10 points to Aaron Hardin, who guessed it first.

For future reference, these genetic puzzles are only slightly more complicated than a Google search. Go to NCBI’s BLAST page, select “nucleotide blast” (because we have nucleotide data), click the box for “others” to get you out of the human genome, enter the sequence in the search box, and click the “BLAST” button.  Any significant matches should be returned from the database within a few seconds.

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invertebrata1

The above pie chart shows the relative proportions of described species in various groups of organisms.  As we can see, most species are invertebrate animals.  Things like snails, flatworms, spiders, sponges, and insects.

Now compare that slice of pie to the proportion of GenBank sequences that represent invertebrates:

genbank Yes, that thin blue wedge is all we’ve got.  While most mammal species have had at least a gene or two sequenced, the vast majority of non-vertebrate species have yet to meet a pipettor.   Entire families of insects haven’t received even a cursory genetic study.

Of course, we make great progress with the efficiency of focusing our efforts on a small number of model organisms.  But surely there’s an opportunity cost of putting all our eggs in the mammal basket.  What about the rest of life?

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Plazi.org launched

http://plazi.org/

Donat Agosti’s group has launched Plazi, a set of tools that translates flat paper taxonomy into dynamic web content. This technology is significant: it means the content of old literature can be extracted automatically into databases. Taxonomic names are tracked and linked to external information, and collecting locations are linked to maps. This will be a valuable time-saver for taxonomic research.

As an example, my doctoral thesis was a fairly traditional piece of work: a book length taxonomic revision, all done in flat text on a word processor. Plazi has turned it into a hyper-linked bonanza of information. If you’re having difficulty appreciating the coolness here, scroll down to the “Material examined” section and click through the localities to view them on Google maps.

Incidentally, I never appreciated the leadership that myrmecology has shown in the emerging field of bioinformatics until I switched from ant research to beetles. I’d grown accustomed to having all our taxonomic literature online, a comprehensive catalogue of species, and a first-rate database of specimen images. Most groups of organisms have nothing of the sort. Many beetle taxonomists still have to sort through file cabinets looking for this paper or that paper, often without an organized catalogue of species to guide them. We’re really quite spoiled.

Here’s more:
Antbase’s Plazi Release statement.

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