bioinformatics
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, 2006Although, I certainly didn't believe it. Truly in nature, it can be described as nonpareil.
With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my own eyes when I saw this structure.
Yet here is, on the screen, parallel DNA.
The image that I posted a couple of days ago came from this same structure. In that image, I hid the rest of the bases, to make it easier to see why this structure is so strange.
Here are some images that show the landmarks a bit better. I hid the hydrogens and used different rendering styles to portray the backbone and the…
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…
terrasig | June 15, 2006So, as a Sb newbie, I'm just figuring out the scheduling around here and saw that tomorrow's new 'Ask A ScienceBlogger' question has already been posted. Hence, I figured I should probably answer last week's question:
Assuming that time and money were not obstacles, what area of scientific research, outside of your own discipline, would you most like to explore? Why?
My SiBlings all took different approaches on this one, with some finding it a poor question because we already probably put a lot of thought into what we're working on now and stay in that area because we love it so much.
I took…
mikethemadbiologist | June 13, 2006In response to this question asked of us by our Seed Overlords (the readers), Steinn says that he would do bioinformatics. As a biologist, I'm really unclear as to what bioinformatics actually is, other than a word you put into your grants to get funding. Let me add that I'm the PI on a federally-funded bioinformatics grant, so I'm supposed to be an expert in this area.
As I see it, bioinformatics usually means one of three things:
The generation of large (massive, actually) datasets.
The analysis of large data sets, and development of computational tools to handle these large datasets.…