Bioinformatics

It's time for the annual blog about the annual Nucleic Acids Research (NAR) database issue. This is the 24th database issue for NAR and the seventh blog for @finchtalk. Like most years I have no idea what I'm going to write about until I start reading the new issue. Something always inspires me. This year's inspiration came from missing data.

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Computers, biological data (molecular sequences, structures, and other data), websites, and databases are integral to modern research. Innovations like precision, or personalized medicine, expect a certain level of patient participation, and our future food and environmental sustainability will require that society can access a multitude of computer-based resources. Thus, higher education has an important role in providing students with employable skills as well as the ability to use data to make important personal and societal decisions. Toward that goal it is worthwhile ... Read more

Pull a spaghetti noodle out of a box of pasta and take a look.  It's long and stiff.  Try to bend it and it breaks.  But fresh pasta is pliable.  It can fold just like cooked noodles. When students first look at an amino acid sequence, a long string of confusing letters, they often think those letters are part of a chain like an uncooked spaghetti noodle.  Stiff and unbending, with one end far from the other. Molecular modeling apps let us demonstrate that proteins are a bit more like fresh pasta. If we apply rainbow colors (Red Orange Yellow Blue Indigo Violet) to a protein chain, we can ... Read more
Sometimes when you go digging through the databases, you find unexpected things. When I was researching the previous posts on insulin structure and insulin evolution, I found something curious indeed.

On pinene and inhibiting enzymes. People of a certain age may remember a series of really funny commercials featuring Euell Gibbons and his famous question about whether you've ever eaten a pine tree.  "Some parts are edible" said Euell. Perhaps some parts are, but other pine tree products aren't so nourishing.  Crystallography365, aka @Crystal_in_city  had a couple of fun blog posts about pinene, ... Read more

In my last post, I wrote about insulin and interesting features of the insulin structure.  Some of the things I learned were really surprising.  For example, I was surprised to learn how similar pig and human insulin are.  I hadn't considered this before, but this made me wonder about the human insulin we used to give to one of our cats.  How do cat and human insulin compare? It turns out, that all ... Read more
What’s the first you think about when you see a spider?  Running away?  Danger?  Fairies? Spiderman? spider and webDo you wonder if spider silk is really strong enough to stop a train, like they showed in Spiderman 2? Whatever your thoughts, you’re probably not thinking about 3D printing in space ... Read more

A few weeks back, we published a review about the development and role of the human reference genome. A key point of the reference genome is that it is not a single sequence. Instead it is an assembly of consensus sequences that are designed to deal with variation in the human population and uncertainty in the data. The reference is a map and like a geographical maps evolves though increased understanding over time.

From the Wiley On Line site: ... Read more

In our series on why $1000 genomes cost $2000, I raised the issue that the $1000 genome is a value based on simplistic calculations that do not account for the costs of confirming the results. Next, I discussed how errors are a natural occurrence of the many processing steps required to sequence DNA and why ... Read more

By @finchtalk (Todd Smith)

We kick off 2014 with Finchtalk’s traditional post on the annual database issue from Nucleic Acids Research (NAR). Biological data and databases are ever expanding. This year was no exception as the number of databases tracked by NAR grew from 1512 to 1552. In the leadoff introduction [1] the authors summarize this year’s issue and the status of the NAR index. The 21st issue includes 185 articles with 58 new databases and 123 updates. In the 1552 database repository, 193 had their URLs corrected and 24 were removed because they were deemed obsolete. ... Read more

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