Bioinformatics

and what is the volume of the sea? This sounds a bit like the beginning of a poem but it's really the answer to the question we posed last week on a Digital Biology Friday. i-3faa77de2c8e6cc50b5fa2cbca9c38b0-rainbow_direction.pngWe can see, in the sequence window, that two strands are both labeled 5' on the left ... Read more
Modified from the original post. i-e0bb5e70117b600f9bf2a270d7bc69f1-telomere1.gifPlaying around with molecular structures is one of the more entertaining activities that you can do with digital biology. I've become totally entranced with molecular structures, both because they're a fascinating art form and because every structure has its own story. I learned this because I ended up writing 69 different structure stories for ... Read more
Today, we're going to look for rainbows in double-stranded DNA and see what they can tell us about DNA structure. First, we're going to get a structure for a double-stranded molecule of DNA and open it in Cn3D. 1K9L If you want to do this at home and you haven't already downloaded a copy of Cn3D, you may want to read these instructions and get a copy. These directions ... Read more
Why do I love Cn3D? Let me count the ways. What does Cn3D do? (Hint: say "Cn3D" out loud). Seriously, Cn3D is a program that draws lovely pictures of molecular structures by using experimental data from techniques like X-ray crystallography and nuclear magnetic resonance spectroscopy. Surprisingly (to some), and in contrast to many bioinformatics programs, Cn3D is really easy and fun to use. Have you ever used programs like MS Office? Using Cn3D is at least 10 times easier. An added benefit is that you don't have to try and find old copies ... Read more
No 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 ... Read more
If 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. i-bed5846063bbebc59fa0a4516d917562-small_mito_mut.gif We also learn something about the ... Read more
Like 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 ... Read more
Did 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. ... Read more
Have you ever wondered how people actually go about sequencing a genome? If they're sequencing a chicken genome, do they raise chickens in the lab and get DNA from the eggs? Does the DNA sequence come out in one piece? Why is there so much talk about computers? What are Phred, Phrap, and Consed? What is the Golden Path? Wonder no more! You too, can take a virtual tour of the Washington University Genome Center. I found this really excellent series of short videos that ... Read more
In 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 ... Read more

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