sequence analysis
sporte | August 17, 2006When can a really bad virus be used to do something good?
When we can use it to learn.
The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as clearly as HIV. In this series, I'm going to guide you through some experiments on HIV evolution that you can do yourself. You won't even have to put on any special clothing (unless you want to), wash glassware or find an autoclave. And, you don't need to any UNIX commands or borrow a…
sporte | August 11, 2006During these past couple of weeks, we've been comparing mitochondrial DNA sequences from humans and great apes, in order to see how similar the sequences are.
Last week, I got distracted by finding a copy of a human mitochondrial genome, that somehow got out of a mitochondria, and got stuck right inside of chromosome 17! The existence of this extra mitochondrial sequence probably complicates some genetic analyses. One of my readers also asked an interesting question about whether apes have a similar mitochondrial sequence in their equivalent of chromosome 17, and how it compares. We will…
sporte | August 10, 2006It's hard sometimes when you're out of synch with the rest of the world. While my fellow ScienceBloggers have been obsessing about breasts, I've been really amused by the genetics of ear wax.
Eh, what's that you say?
Yes, it's true. Back in March, when Nature Genetics published this paper from Yoshiura (and friends), this bit of fun just went in one ear and out the other. But then I read this really funny blog about a person, some ear wax, and an NMR machine, and well, you guessed it, I couldn't resist.
To me, it's been a jelly bean flavor that I studiously try to avoid. To several…
sporte | August 4, 2006Last week, we decided to compare a human mitochondrial DNA sequence with the mitochondrial sequences of our cousins, the apes, and find out how similar these sequences really are.
The answer is: really, really, similar.
And you can see that, in the BLAST graph, below the fold.
A quick glance shows that the ape with the most similar mitochondrial sequence is Pan paniscus, the pigmy chimpanzee. Next, is Pan troglodytes, the chimp that we see in movies, and last we have Gorilla gorilla.
Then we have a really curious, and unexpected, matching sequence.
Click the picture to see a larger…
sporte | July 28, 2006We've had a good time in the past few last weeks, identifying unknown sequences and learning our way around a GenBank nucleotide record. To some people, it seems that this is all there is to doing digital biology. They would, of course, be wrong.
We can do much, much more than identifying DNA sequences and obtaining crucial information, like who left their DNA behind on that little blue dress.
Today, we're going to a deeper question about who we are and who are our relatives.
Drumroll, okay, here it comes:
How similar are DNA sequences between humans and apes?
Your assignment is to find…
sporte | July 24, 2006A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students gather environmental samples from different campus ecosystems, isolate DNA, amplify 16s ribosomal DNA by PCR, and check their PCR results by gel electrophoresis.
DNA samples are next sent to the university's Genetic Resources Core Facility , where scientific staff, in…
sporte | July 21, 2006"Hey Rocky, watch me pull a rabbit out of my hat!"
I realized that I should add just a bit more information to last answer on gene identification, so here it is.
After the last installment, Diego commented:
but still you do not know exactly what part of your DNA sequence is matching to the annotated protein.
Ahh, but we do.
And I was negligent in not showing you.
There are multiple ways to view the GenBank record that we arrived at while following links from our matching sequence.
A very handy way, especially if you're looking at where sequences align to a larger subject sequence, like…
sporte | July 21, 2006Welcome back!
If you've just joined us, we're in the middle of a quest to find the identity of an unknown nucleotide sequence. To summarize our results so far, we used this sequence to do a blastn search of GenBank, using all the default settings at the NCBI. You can see the beginning of the project here.
And we had some rather curious results.
It appeared that our sequence matched sequences from very diverse organisms, like Dengue virus, E. coli, and Simian Immunodeficiency virus. Very strange!
There was another curious word, too, that appeared in the descriptions for each of the results…
sporte | July 14, 2006Last week, we embarked on an adventure with BLAST.
BLAST, short for Basic Alignment Search Tool, is a collection of programs, written by scientists at the NCBI (1) that are used to compare sequences of proteins or nucleic acids. BLAST is used in multiple ways, but last week my challenge to you, dear readers, was to a pick a sequence, any sequence, from a set of 16 unknown sequences and use BLAST to identify that sequence.
This week, we'll examine the results.
I did the experiment, too, with a completely different unknown sequence that's pasted below. This sequence is not part of the data…
sporte | July 10, 2006How did the human genome ever get finished if every one of the three billion bases had to be reviewed by human eyes?
In the early days of the human genome project, laboratory personnel routinely scanned printed copies of chromatograms, editing and reviewing all DNA sequences by eye. For more background, see the post on qualitative measures of DNA quality.
Later on, when the genome sequencing turned into a race, and the pace of DNA sequencing began to increase, some genome centers realized that it was too expensive and time consuming to have Ph.D. scientists, or even technicians, review all…
sporte | July 5, 2006What do genetic testing and genealogy have in common?
The easy answer is that they're both used by people who are trying to find out who they are, in more ways than one.
Another answer is that both tests can involve DNA sequence data.
And that leads us to another question. If the sequence of my mitochondrial DNA is only two bases different from Cleopatra's, am I really a distant relative? And how do I really even know that my mitochondrial DNA is only two bases different in the first place? What does having a DNA sequence really mean?
Students sequencing mitochondrial DNA
I wrote earlier…