sequence analysis

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.

Every fall, we had to confront it. People would let their dogs run around on the field in the morning and by the time soccer practice started, the field would be full of deadly doo.

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Koko

There's nothing that hurts soccer practice more than a soccer ball or shoes that went through a pile of dog poo. ... Read more

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
A few days ago, I wrote about a cool project that some high school students did where they used DNA sequencing to identify seafood. One question that came up from one of my commenters was how a school would start a project like this. I'm totally biased, but I think DNA sequencing (well, actually the data analysis) is one of the most interesting things that a class can do as part of a research project. These days, getting started with this kind of project, wouldn't be so hard. Here's are ... 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

Ancestry tests aren't just for humans anymore. We went to Petco this weekend to buy dog food and found brochures for doggy DNA testing. Now, those of you with dogs of uncertain parentage need puzzle no longer. According to Petco, their SNP test (what is a SNP?) can identify over 100 different breeds and they'll tell you which breeds are represented in your dog and whether your dog's breeding is mixed (or pure). ... Read more

This the third part of case study where we see what happens when high school students clone and sequence genomic plant DNA. In this last part, we use the results from an automated comparison program to determine if the students cloned any genes at all and, if so, which genes were cloned. (You can also read part I and part II.) Did they clone or not clone? That is the question. ... 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
In its simplest sense, we imagine that learning occurs through a series of positive and negative rewards. Some actions lead to pleasure, others to pain, and it seems reasonable to expect that people will repeat the actions with pleasurable results and avoid those that ended in pain. Yet, we all know people who aren't deterred by the idea of punishment. We all know people who never seem to learn. Could there be a physical reason, hidden in their genes? In December 2007, Science published a study by Klein et. al. (1) where they asked if a specific genotype at a location ... Read more

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