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A long standing debate in my field is whether or not biologists, who work with computers, need to learn how to program. I usually say “no.” Let the programmers program, the biologists interpret the results, and let everyone can benefit from each other’s expertise. Well, I’ve changed my mind in one respect. Most biologists need…

DNA sequence traces are often used in cases where: We want to identify the source of the nucleic acid. We want to detect drug-resistant variants of human immune deficiency virus. We want to know which base is located at which position, especially where we might be able to diagnose a human disease or determine the…

Last year I wrote about an experiment where I compared a human mitochondrial DNA sequence to primate sequences in the GenBank. Since I wanted to know about the differences between humans, gorillas, and chimps, I used the Entrez query ‘Great Apes’ to limit my search to a set of sequences in the PopSet database that…

Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who’s around by looking at bits of their genome. Researchers are using this approach to find the culprit that’s killing the honeybees. We’re…

The simple fact is this: some DNA sequences are more believable than others. The problem is, that many students and researchers never see any of the metrics that we use for evaluating whether a sequence is “good” and whether a sequence is “bad.” All they see are the base calls and sequences: ATAGATAGACGAGTAG, without any…

We have lots of DNA samples from bacteria that were isolated from dirt. Now it’s time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we’re using many of the same principles.

The next time you bite into a crisp juicy apple and the tart juices spill out around your tongue, remember the honeybee. Our fall harvest depends heavily on honeybees carrying pollen from plant to plant. Luscious fruits and vegetables wouldn’t grace our table, were it not for the honeybees and other pollinators.

Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?

California Burning!

The NASA Earth observatory has some amazing photos of the wildfires in California. I’ve put a small version of one image here, but you should go to the NASA site and see the high resolution images. The fires are horrible but the images are fantastic.

Welcome Bio256 students! This quarter, we’re going to do some very cool things. We are going to use bioinformatics resources and tools to investigate some biological questions. My goal, is for you to remember that these resources exist and hopefully, be able to use them when you’re out working in the biotech world. I don’t…