Influenza resources

Nick's post on Amantadine resistance in swine flu was so interesting, I had to look at the protein structures myself.

I couldn't find any structures with the S31N mutation that Nick discussed, but I did find some structures with the M2 protein and Amantadine. Not only are these structures beautiful, but you can look at them and see how the protein works and how the drug prevents the protein from functioning.

As Nick mentions, the M2 protein from influenza ... Read more

No more delays! BLAST away!

Time to blast. Let's see what it means for sequences to be similar. 

First, we'll plan our experiment.  When I think about digital biology experiments, I organize the steps in the following way: 

           A.  Defining the question

B.  Making the data sets

           C.  Analyzing the data sets

D.  Interpreting the results

I'm going intersperse my results with a few instructions so ... Read more

We'll have a blast, I promise! But there's one little thing we need to discuss first...

I want to explain why I'm going to use nucleotide sequences for the blast search. (I used protein the other day). It's not just because someone told me too, there is a solid rational reason for this.

The reason is the redundancy in the genetic code.

Okay, that probably didn't make any sense to those of you who didn't already know the answer. Here it is. ... Read more

We had a great discussion in the comments yesterday after I published my NJ trees from some of the flu sequences. If I list all the wonderful pieces of advice that readers shared, I wouldn't have any time to do the searches, but there are a few that I want to mention before getting down to work and posting my BLAST results. Here were some of the great suggestions and pieces of advice; 1. Do a BLAST search. Right! I can't believe I didn't do that first thing, I think the ... Read more
We were joking about this a couple of hours ago, but I just picked up the phone and learned that two middle schools will be closed for the week. Aki Kurose and Stevens middle schools are closed from tomorrow to May 8th. Yikes!Read more

Last night, the phone rang at 9:22 pm. I quickly glanced at the caller ID. Hmmm. Why is the Seattle School district calling us at this time of night?

Apparently the swine flu has come to Seattle and the school district thought we should know.

Those messages are helpful if you're a parent, but they don't tell much about the rest of the world.

Health Map is a really wonderful, user-friendly, resource for following the epidemic.


... Read more

What tells us that this new form of H1N1 is swine flu and not regular old human flu or avian flu?

If we had a lab, we might use antibodies, but when you're a digital biologist, you use a computer.

Activity 4. Picking influenza sequences and comparing them with phylogenetic trees

We can get the genome sequences, piece by piece, as I described in earlier, but the NCBI has other tools that are useful, too.

The Influenza Virus Resource will let us pick sequences, align them, and make trees so we can quickly compare the sequences to ... Read more

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
I'm a big of learning from data. There are many things we can learn about swine flu and other kinds of flu by using public databases. In digital biology activity 1, we learned about the kinds of creatures that can get flu. Personally, I'm a little skeptical about the blowfly, but... Now, you might wonder, what kinds of flu do these different creatures get? Are they all getting H1N1, or do they get different variations? What are H and N anyway? We can discuss all of these, but for now, lets see what kinds of flu strains infect different kinds of creatures. Activity 2. What ... Read more

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