Genetics & Molecular Biology

Have you ever wondered how to view and annotate molecular structures? At least digital versions? It's surprisingly easy and lots of fun. Here's a movie I made that demonstrates how you can use Cn3D, a free structure-viewing program from the NCBI. Luckily, Cn3D behaves almost the same way on both Windows and Mac OS X. ... Read more
I read about this in Bio-IT World and had to go check it out. It's called the Genome Projector and it has to be the coolest genome browser I've ever seen. They have 320 bacterial genomes to play with. Naturally, I chose our friend E. coli. The little red pins in the picture below mark the positions of ribosomal RNA genes (It's not perfect, at least one of these genes is a ribosomal RNA methyltransferase and not a 16S ribosomal RNA.) ... Read more
Here's a fun puzzler for you to figure out. The blast graph is here:
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The table with scores is here, click the table to see a bigger image: ... Read more
What do you do after you've used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What's the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics is concerned with fixing data entry errors and spelling mistakes. The parts of this series are: I. Downloading the data from iFinch and preparing it for analysis. (this is the ... Read more
Well, probably getting a stipend to help you do it. And, the really cool thing is that's part of the deal! Hustle, hustle the deadline is March 7th, and all the contact info is below. The NSF Research Experience for Undergraduates program in Environmental Microbiology at UNLV is accepting applications. This grant provides students with the opportunity to work on a research project for a 10 week period with a faculty mentor. Students receive a $4000 stipend, round trip airfare, and housing in a UNLV dormitory. Mentors have projects in the following areas: ⢠... Read more
The New England Journal of Medicine published a study yesterday showing that small changes in the DNA in the long arm of chromosome 16 are associated with autism. i-60b957fad1b9e1a3e306d0c520e02043-kids_singing.jpgI met a teenager with autism last summer, when I attended family night at the Seattle Park and Rec summer camp program for kids with special needs. It's a fantastic program. The kids spend a week or more at summer camp ... Read more
If you look below the fold, you can see two molecules locked in a tight embrace. These molecules or their closely related cousins can be found in any cell because their ability to evolve is slowed by their need to interact with each other in the right way. In an earlier post, I asked: Who are they?
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One partner is a small bit of ... Read more
Genetics textbooks abound with stories of European royalty and the hazards of having children after you've married one of your cousins. It struck me as an interesting parallel that the lion is such a popular symbol in so many royal coats of arms. Like the royal families of Europe, certain lion populations have also suffered from a few too many copies of certain recessive genes. I first read about the Florida panthers a few years ago while researching material for a class that I teach on using bioinformatics. It wasn't my first encounter with ... Read more
You can get a jump on the Darwin Day festivities. Once again the Alliance for Science is sponsoring an essay contest for Darwin Day. If you download their suggestions for good essay writing, you can get your essay done over winter break and have a good crack at winning on those cash prizes!
The Alliance for Science is pleased to announce our second annual National High School Essay Contest. We invite interested students to submit essays of up to 1,000 words on one of two topics -- Climate and Evolution or ... Read more
In which we're reminded that database searches are experiments, too. One of the trickiest things with bioinformatics experiments is repeating them. This challenge isn't related to the validity of the original results, the challenge is that, unless you made your own database and kept it in the same state, the database that you'll be using at a later time, sometimes even a day later, is a different database. And, if you query a different database, you may get a different result. The series that I'm currently posting is one that I started working on a couple of years ago. ... Read more

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