Protein words

In my post about creating a DNA font, I mentioned the idea of doing a similar thing for proteins. There are 20 standard amino acids, each with a single character abbreviation. When combined with symbo... Read More


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Our latest paper on the CE-CP method for finding protein circular permutations is in this month’s issue of Bioinformatics. Spencer E. Bliven, Philip E. Bourne, and Andreas Prlić. (2015) Detecti... Read More

Using BioJava from R

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I’m a fan of literate programming. When I’m writing a paper, I typically use LaTeX to draft the paper, Java to generate the data, and R to create figures and do basic analysis. With Sweave (or the... Read More

ISMB 2014

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I had a great time at the ISMB conference & related events in Boston last week. As always, it is an exciting event scientifically and socially. First there was the Open Bio Foundation’s Cod... Read More


I learned some interesting facts about fetal development recently. So interesting, they can only be properly delivered by Doctor McNinja (using the awesome Dinosaur Comic mashup template)... Read More