Bioinformatics

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 things in GenBank and how this kind of project could be a good sort of discovery, inquiry-based project for biology, microbiology, or bioinformatics students. I. The back story ... Read more

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 a virus came to be part of the Aedes aegypti genome.

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 genome record II. What do the mumps proteins do? And how do we find out? III. ... Read more

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 how do we find out? III. Serendipity strikes when we Blink. IV. ... Read more

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 out? III. Serendipity strikes when we Blink. IV. ... Read more

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 happen. One of the projects that I've been working on during the past couple of years has involved developing educational materials that use bioinformatics tools to look at the isozymes that metabolize alcohol. As part of this ... Read more

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... the mutation mapped in a completely different gene. I presented the data here and wrote a bit about my surprise at finding this mistake and even greater ... Read more

This the second part of three part case study where we see what happens when high school students clone and sequence genomic plant DNA. In this part, we do a bit of forensics to see how well their sequencing worked and to see if we can anything that could help them improve their results the next time they sequence. How well did the sequencing work? Anyone who sequences DNA needs to be aware of two kinds of problems that afflict their results. We can divide these into two ... Read more

What happens when high school students clone and sequence genomic DNA? Background DNA sequencing is a wonderful tool for discovery and a great technique for getting students involved in molecular science. This fall, Bio-Rad will officially begin selling their DNA cloning and sequencing kit. Now, students across the country will have the tools in hand to begin their own projects cloning and sequencing plant genes. Of course, without bioinformatics there's no way to know what's been cloned or sequenced. This is where we come in. As part of an ... Read more