sequence analysis
sporte | May 25, 2007tags: plants, bioinformatics, sequence analysis, viruses, fungi
How does grass grow in the extremely hot soils of Yellowstone National Park? The quest continues.
Read part I, part II, part III, and part IV to see how we got here.
And read onward to see where will we go.
In our last episode, I discovered a new tab in the protein database (well, new to me anyway).
Related structures
If you select this tab, you get a list of protein sequences that are similar, by blastp, to the amino sequences in protein structures.
Naturally, I clicked the tab, and then the Links link, to see…
sporte | May 18, 2007tags: plants, bioinformatics, sequence analysis, viruses, fungi
Quick synopsis: A type of grass grows in Yellowstone National Park in hot (65° C), unfriendly soil. How the plant manages this feat is a mystery. What we do know, is that the grass can only tolerate high temperatures if it's been infected by a fungus, and the fungus has to be infected by an RNA virus. In the paper describing this discovery, the researchers provided the GenBank accession numbers for the viral sequences. I decided to see if I could find out more about the proteins and what they do. Read part I, part II, and part…
sporte | February 21, 2007Grasses 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 introduction
Today: Part III: An inordinate fondness for hypothetical proteins
After today, we will have:
Part IV: Did we get lost in translation?
(I will add the link after it's posted)
Let's begin
Sigh.
It always happens when I have homework to…
sporte | February 8, 2007"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 NCBI) are a result of conceptual translations.
What? !!
A conceptual translation…
sporte | February 7, 2007Yesterday, 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 yesterday. If the fungus wasn't infected, the plants couldn't tolerate high temperatures. And, not only was the fungus-virus combination important for the grass, it had the unusual ability to confer temperature…
sporte | February 2, 2007Vizzini: 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 a completely unexpected way and no one else seems bothered by this!
I had this happen once with the word "artifact." I had organized a conference and some workshop…
sporte | February 1, 2007To 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 sequencing world has it's chimeras, too. There are two main kinds that I know. Sometimes chimeras…
sporte | January 10, 2007I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared to deal with it.
Even the kids aren't looking too happy about it, though. By this time of the school year, they've caught on that every snowday has a price. And, they will pay that price IN JUNE. Already the last day of school has been postponed until the 25th of June.
Who knows? The kids…
sporte | December 22, 2006Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants?
Two reports in Nature (1, 2) suggest that bacterial populations differ between people who are obese and people who not, and that the bacterial inhabitants of their guts, may be partly to blame.
In one study, the authors studied the bacterial populations of their volunteers' intestines by compiling a data set of 18,348 DNA sequences for bacterial 16S ribosomal RNA by sampling feces. Wow! That's a lot of ... well, I won't say it, but you know what I mean. In…
sporte | December 7, 2006Five Bulgarian nurses and a Palestinian doctor (dubbed the Tripoli six) may be executed soon by the Libyan government for the crime of deliberately infecting over 400 children with HIV. If they did infect the children, this would be a horrendous crime. If they did not infect the children, it's the Libyan government that will be killing innocent people.
The clock is ticking.
Some of you might be wondering (I know I was): How exactly is molecular sequence data being used to solve the crime? Why are scientists and science bloggers claiming that the Tripoli six are innocent?
Let's begin by…
sporte | October 10, 2006Why is an eye, an eye and a nose, a nose? Why do different cells create different kinds of tissues when all the cells in a single organism start out with the same set of instructions (aka DNA)?
Head, Shoulders, Knees, and Toes is a learning activity that helps students discover, for themselves, that certain genes are expressed in some tissues but not in others. My goal here, as part of our NSF-funded project, is to show how students can learn biology by doing science with bioinformatics tools.
If you already know all about ESTs, you might want to jump ahead and read about the activity. If…
sporte | September 27, 2006We went on an excursion last weekend to see the Dead Sea Scrolls at the Pacific Science Center. None of us could resist going downtown to look at written texts over 2000 years old. Uncovered in 1946, by a Bedouin shepherd, the scrolls have had an interesting history over the past 50 years, most of it out of the public eye. Only recently, have a large number of scholars and members of the public been granted access.
We're still kind of amazed that they came to Seattle.
I'm fascinated by archeology, but I was also interested in how DNA analysis is being used to study the scrolls and…
sporte | September 26, 2006Razib inspired me to share some of the story behind why white people are considered derivatives.
Reposted from the Classic Digital Bio.
No red herrings, here! Lamason et. al. found a single gene that controls human skin color while studying pigmentation in zebra fish (1).
These zebra fish had an unusual golden color that turned out to be an important clue. Lamason and collaborators found that the golden zebra fish lost their normal color because of a mutation in the slc24a5 gene. When the zebra fish have the mutant form, they produce fewer melanosomes.
A short language lesson
Fewer…
sporte | September 7, 2006No biology course is complete these days without learning how to do a BLAST search.
Herein, I describe an assignment and an animated tutorial that teachers can readily adopt and use, and give teachers a hint for obtaining the password-protected answer key.
Development of the tutorial and the activity were supported by funding from the National Science Foundation.
This is reposted from the the original DigitalBio blog.
This popular activity, designed to accompany the BLAST for beginners tutorial, has been updated to incorporate student comments and teacher requests. Originally developed for…
sporte | September 1, 2006If we compare sections 1, 2, and 3, we see that section 2 matches very well in a number of different samples, and that there are differences between the sequences in sections 1 and 3.
We also learn something about the people who did the experiment.
At first it appears somewhat odd that there are many matching sequences that are all shorter than the genome and all the same length.
What's up with that?
It turns out that information doesn't have anything to do with the fraction of the genome that matches our query. These short segments are PCR products. They're the same size because the PCR…
sporte | August 25, 2006Like biology, all bioinformatics is based on the idea that living things shared a common ancestor. I have posted, and will post other articles that test that notion, but for the moment, we're going to use that idea as a starting point in today's quest.
If we agree that we have a common ancestor, then we can use that idea as a basis to ask some interesting questions about our genomes. For, example, we know that genomes change over time - we've looked at single nucleotide changes here and here, and we've seen that large chunks of DNA can move around here.
So, it's interesting to consider…
sporte | August 23, 2006Did HIV become resistant to Atazanavir because of a genetic change?
Was that genetic change inherited?
Did HIV evolve?
Can we explain why genetic changes at specific sites might help HIV escape the effects of the drug?
Let's find out.
All of the sequences in the image below (except for the first) come from HIV strains that were isolated from patients who took Atazanavir and no other protease inhibitors. All of the strains of HIV from patients were resistant to the drug.
If an amino acid is different from other strains, the color at that position is changed. Since we see different…
sporte | August 21, 2006In which we see the results and come to our own conclusions.
If you want to let other people tell you what's right and what's wrong, they will surely do so. Turn on the TV and hordes of happy actors bounce around, only too happy to help you purchase the right deodorant. Open your e-mail and everyone wants to share the best on-line pharmacy and investment guide.
Ugh.
I prefer making my own decisions, thank you very much.
So, I want to give you a chance to look at the data and decide for yourself, if the data show HIV protease sequences changing over time.
Let's see the results.
We're…
sporte | August 19, 2006Let the experiment begin.
We're experimenting with HIV in this series. And yes, you can try this at home!
If you want to see where we've been and get an idea where we're going, here are the links.
Part I. Meet HIV and learn how we're going to use it look at evolution. An introduction to the experiment and a link to a short flash movie on HIV.
Part II. Instructions for doing the experiment.
Part III. Look at the sequence results.
Part IV. Look at protein structures and see if we can explain why the experiment worked the way it did.
Let's move onward.
1. I made a data set of amino acids…
sporte | August 18, 2006The past few Fridays, we've been comparing human mitochondrial DNA with the mitochondrial DNA of different apes.
We started doing this here, where you can find directions for getting started.
And, we've found some interesting things.
In this installment, we found that humans have practically an entire mitochondrial genome stuck in chromosome 17.
Last week, we found that human mitochondrial DNA is more similar to that of chimpanzees than to gorillas. We found that 90.6% of the bases in human mitochondrial DNA match bases in the Bonobo chimp and 90.7% match bases in the Chimpanzee.
This…