sequence analysis

This afternoon, I was working on educational activities and suddenly realized that the H1N1 strain that caused the California outbreak might be the same strain that caused an outbreak in 2007 at an Ohio country fair. UPDATE: I'm not so certain anymore that the strains are the same. I'm doing some work with nucleic acid sequences to look further at similarity. Here's the data. Once I realized that the genome sequences from the H1N1 swine flu were in the NCBI's virus genome resources database, I had to take a look. And, like eating potato chips, making ... Read more
I was pretty impressed to find the swine flu genome sequences, from the cases in California and Texas, already for viewing at the NCBI. You can get them and work them, too. It's pretty easy. Tomorrow, we'll align sequences and make trees. Activity 3: Getting the swine flu sequence data 1. Go to the NCBI, find the Influenza Virus Resource page and follow the link to: 04/27/2009: Newest swine influenza A (H1N1) sequences. 2. You'll see a page that looks like this: ... Read more

Watching the chIPs roll in, then I watch them roll away again, I'm just sitting on the DNA, wasting time (sung to the tune of "Sitting on the dock of the bay" by Otis Redding) Hesselberth et.al. recently published a paper about digital genomic footprinting that blew me away because it has so much potential. The authors used DNAse I and Next Generation DNA Sequencing to map every site in the yeast genome where a protein might be sitting. Since I used to do similar kinds of experiments, albeit on a much, much smaller scale, this sort of publication boggles my mind. ... Read more

In which we identify unknown human proteins.

Yesterday, I wrote about using the BLOSUM 62 matrix to calculate a score for matches between two proteins. Those scores give us a good start on understanding how blastp determines whether two sequences are matching by chance or because they're more likely to be related. But that's not all there is to calculating a blast score, and there's at least one other statistic to consider as well, the E value.

It all
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In which we search for Elvis, using blastp, and find out how old we would have to be to see Elvis in a Las Vegas club.

Introduction
Once you're acquainted with proteins, amino acids, and the kinds of bonds that hold proteins together, we can talk about using this information to evaluate the similarity between protein sequences. We can easily imagine that if two protein sequences are identical, then those proteins would have the same kind of activity. But what about proteins that are similar in some regions, and not others, or proteins that only ... Read more

Ebola virus has impressed me as creepy ever since I read "The Hot Zone: A Terrifying True Story some years back by Richard Preston. (I guess he has a new book, too, ... Read more
One of the holy grails of modern medicine is the development of a vaccine against HIV, the virus that causes AIDs. An obstacle to attaining this goal has been the difficulty in stimulating the immune system to make it produce the right kinds of antibodies. A recent finding in Science describes a gene that controls production of these antibodies and may provide insights to the development of an effective vaccine. (1). Antibodies are special kinds of proteins that bind to things, often very tightly. If they bind to the right molecules, they can prevent viruses from infecting ... Read more
Let's play anomaly! Most of this week, I've written about the fun time I had playing around with NCBI's Blink database and finding evidence that at least one mosquito, Aedes aegypti, seems to have been infected at some point with a plant paramyxovirus and that the paramyxovirus left one of its genes behind, stuck in the mosquito genome. During this process, I realized that the method I used works with other viruses, too. I tried it with a few random viruses and sure enough, I found some interesting things. You've got a week to give it a try. Let's see ... Read more
Lots of bloggers in the DNA network have been busy these past few days writing about Google's co-founder Sergey Brin, his blog, his wife's company (23andme), and his mutation in the LRRK2 gene. I was a little surprised to see that while other bloggers (here, here, ... Read more
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

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