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Digital Biology Fridays

Category archives for Digital Biology Fridays

Let’s play anomaly!

Here’s a fun puzzler for you to figure out. The blast graph is here:

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…

Last week I posted an image with two molecules (below the fold), one protein and one nucleic acid, and asked you about the probability of finding similar molecules in different species. You gave me some interesting answers.

This is a fun puzzle. The pink molecule is a protein and the other molecule is a nucleic acid.

As many of you know, I’m a big fan of do-it-yourself biology. Digital biology, the field that I write about, is particularly well-suited to this kind of fun and exploration. Last week, I wrote some instructions for making a phylogenetic tree from mitochondrial genomes. This week, we’ll continue our analysis.

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…

During the past few Fridays (or least here and here), we’ve been looking at a paper that was published from China with some ?-lactamase sequences that were supposedly from Streptococcus pneumoniae. The amazing thing about these particular sequences is that ?-lactamase has never been seen in S. pneumoniae before, making this a rather significant (and…

I began this series last week with a question about a DNA sequence that was published and reported to be one the first beta-lactamases to be found in Streptococcus pneumoniae. Mike has a great post about one of problems with this paper. I think the data themselves are awfully suspicious.

Last Friday, we had another in the series of weird DNA structures. (You can see the first here). I asked the audience to identify the unusual feature in this molecule. Here’s the first picture: tags: DNA structure, DNA , molecular structure, biochemistry Here’s the answer: