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Databases

Category archives for Databases

Do mosquitoes get the mumps? Part V. A general method for finding interesting things in GenBank This is the last in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes and a general method for finding other interesting things. In this last part, I discuss a general method for finding novel…

Part 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…

Part III. Serendipity strikes when we Blink In which we find an unexpected result when we Blink while looking at the mumps polymerase. This is the third in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes. And yes, this is where the discovery happens. I. The back story from the…

Part II. What do mumps proteins do? And how do we find out? This is the second in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes, and a general method for finding interesting things. I. The back story from the genome record II. What do the mumps proteins do? And…

Part I. The back story from the genome record Together, these five posts describe the discovery of a novel paramyxovirus in the Aedes aegyptii genome and a new method for finding interesting anomalies in GenBank. I. The back story from the genome record II. What do the mumps proteins do? And how do we find…

PubMed is an on-line database at the National Center for Biotechnology Information (NCBI) that contains information from scientific literature. Most of the information is related to medical research. To search PubMed, you use a program called Entrez. You go to the NCBI, select PubMed from the menu, type words into the text box, and start…

One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it’s really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that sometimes this reconciliation may never…

Instead of enjoying a sunny summer day today, or partying with SciBlings in New York, I’m staring out my window watching the rain. Inspiration hit! What about searching for August? Folks, meet the HFQ protein from E. coli. I found this lovely molecule by doing a multi-database search at the NCBI with the term ‘August‘.

A few weeks ago, I wrote about a paper in Science(1) that I read on a connection between a mutation in the dopamine D2 receptor and the genetics of learning. Only, it turned out that when I looked at the gene map…

or is it just an idea that’s ahead of the curve?