genbank
awild | April 6, 2010Plega 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…
awild | December 11, 2008
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:
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…
sporte | September 24, 2008Part IV. Assembling the details and making the case for a novel paramyxovirus
This is the fourth in a five part series on an unexpected discovery of a paramyxovirus in a mosquito. In this part, we take a look at all the evidence we can find and try to figure out how a gene from a virus came to be part of the Aedes aegypti genome.
image from the Public Health Library
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a novel mosquito paramyxovirus
V. A…
sporte | April 1, 2008Is it real or is it April Fools?
The March 21st issue of Science has an interesting news article by Elizabeth Pennisi and a letter to the editor about a proposal to wikify GenBank. Currently, the NCBI holds the original authors responsible for editing or correcting entries and this does cause problems when those authors fail to return to the scene and fix what they've submitted. Some researchers are suggesting that third parties be allowed to fix some of those mistakes or at least add comments to records, to warn the unwary.
There are some good arguments on both sides and it's certainly…