classroom activities

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

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

Genome sequences from California and Texas isolates of the H1N1 swine flu are already available for exploration at the NCBI. Let's do a bit of digital biology and see what we can learn. Activity 1. What kinds of animals get the flu? For the past few years we've been worrying about avian (bird). Now, we're hearing about swine (pig) flu. All of this news might you wonder just who gets the flu besides pigs, birds, and humans. We can find out by looking at the data. Over the past few years, researchers have been sequencing influenza genomes and depositing ... 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 ... Read more

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

Cofactor Genomics is offering to sequence a genome for a few classes for free using Next Generation DNA Sequencing technology (either Illumina GA or via AB SOLiD). Quoting from their site:

Cofactor will ask course organizers for a 1 page description of how their ~700Mb sequencing project could be used as an effective teaching aid in their class. We will review and choose the best entries during the month of May. Those entries will be awarded a free sequencing project ... Read more

The grocery store magazine covers all say that home made gifts are big this year. So I thought, some of you might like to channel your inner Martha Stewart and make gifts with a science theme. Reposted in honor of the holiday and the economy. I'm here to help to you make a merry mug with one of our favorite molecules. Yep, we're talking caffeine. 1. First, we'll go to ... Read more

I just love this title! It's nerdy and cute, all at the same time. I read about this in www.researchblogging.org and had to check out the paper and blog write up from The Beagle Project (BTW: some of you may be interested in knowing that The Beagle Project is not a blog about dogs.) The paper describes a class where students from Marseilles University investigate the function of unidentified genes from a ... 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