Bioinformatics

Registration has opened a bit late this year, but it's always tricky when large programs change hands. The Chautauqua Short Course program for College Teachers is no different. In fact, as far as I know, we may still be waiting for the National Science Foundation to make a final decision on funding. Still, summer is rapidly approaching and I know many of you are making plans for attending summer workshops and squeezing in a bit of vacation time. That's why I think you might like to consider learning bioinformatics in Alaska. ... Read more

Grasses at Yellowstone National Park are able to grow temperatures (65°; C) that would toast most living things. Step right up! Watch original research, as it happens, on the web! I'm going to use bioinformatics to see if I can find that answer to the puzzle of heat-tolerant plants. Previous parts:

• Part I. The research
• Part II. An
... Read more

I found it in the MeSH database. Really! Looking for a quick answer? Don't ask a scientist It doesn't take long to realize that scientists can spend countless hours debating the meaning of words. Our very own ScienceBlogs is a great example, just look at the many ways we can define (and debate) the meaning of a small, four-letter word like "gene". We also like to qualify our answers with a thousand conditions "usually, it's like this, but...." This ... Read more

"Beware the Jabberwock, my son! The jaws that bite, the claws that catch! Beware the Jubjub bird, and shun The frumious Bandersnatch!" - from Jabberwocky, by Lewis Carroll

I'm certain that if we ever sequenced DNA from the frumious Bandersnatch it would match hypothetical and putative proteins.

Why? Because we always (well, almost always) get matches to hypothetical and putative proteins when we do a database search with a protein sequence.

Why? Because many of the protein sequences in GenBank (at the ... Read more

Yesterday, both Joshua and I wrote about grasses that grow in the unusually hot soil at Yellowstone National Park. Now, I knew that hot springs bacteria can tolerate high temperatures, but I was really surprised to learn that plants could. It was even more surprising to learn that this amazing ability was conferred on the plants by an infected fungus. I presented the data ... Read more

How to win the X PRIZE in genomics In October, 2006, the X PRIZE foundation announced that second X prize would focus on genomics. The first team to successfully sequence 100 human genomes in 10 days will win $10 million dollars. And I would venture to guess, that the winning team would also win in the IP (intellectual property) game and the genetic testing market since they will gain an unprecedented look at genetic variation. But when is done really done? The first ... Read more

Vizzini: He didn't fall? Inconceivable! Inigio: You keep using that word. I do not think it means what you think it means. - William Goldman, The Princess Bride

Excuse me while I temporarily interrupt the genome sequencing series to define a word. Artifacts in the classroom It's disorienting. You learn a word in certain context. You're sure of it's meaning and then you end up in a situation where people use the word in ... Read more

To the ancient Greeks, a chimera was a kind of monster, with the body of a goat, the tail of a dragon, and a lion's head. To geneticists, a chimera can be an animal that's derived from two embryos, such as a transgenic mouse. Or if the organism is a plant, it can be a plant with a graft. We have a chimeric cherry tree in our back yard with branches from Rainier cherries, Bing cherries, and Van cherries. And you should see the chimeras that hang out at evolgen. Naturally, the DNA cloning and ... Read more

The general steps in genome sequencing were presented in the earlier installments ( there are links at the bottom of the page), but it's worth repeating them again since each of the earlier steps has a bearing on the outcome of those that come later. These are:

• Break the genome into lots of small pieces at random positions.
• Determine the sequence of each small piece of DNA.
• Use an assembly program to figure out which pieces fit together.

That first step, making a collection of DNA fragments (a library), with breakpoints at random positions is of ... Read more

"How much do I love you? I'll tell you no lie. How deep is the ocean? How high is the sky?" - Irving Berlin The other installments are here: Part I: Introduction Part II: Sequencing strategies Part III: Reads and chromats ... Read more