A new online viewer for multiple alignments

For my work on the alignment of coiled-coil proteins, I needed an alignment viewer that could highlight coiled-coil domains, since they contain less phylogenetic signal than other parts of the protein. Adding this to JalView seemed very complicated, and not possible at all in other web-based viewers like MView. I therefore created amview (for "annotated multiple alignment viewer"), which looks like this in practice:

Shown is the MSA for spd-5 (and here is the entry in my coiled-coil orthologs database). Amino acids are colored according the ClustalW rules, coiled-coil residues are in a lighter color (and the "a" register of the heptad repeat is underlined). Below, two interaction domains are shown. At the very bottom, a small chart shows the degree of conservation across the whole alignment, which can be used to quickly scroll to the conserved regions. The cog on top hides two options: you can hide columns with too many gaps, and proteins that seem to be fragments.

I've only tested this thoroughly in Google Chrome, as I found other browsers to be too slow. Still, it's better than loading a Java applet, and even runs on iPhones/iPads etc.! The implementation relies on Django on the server side, and JavaScript / JQuery in the browser.

Announcing SIDER: a database of side effects

After using side effects to predict drug targets, we now created a public database of side effects with a total of 62269 side effects for 888 drugs. The database was created by doing text-mining on labels from various different public sources like the FDA. Furthermore, I developed rules to extract frequency information from the labels, this worked for about one third of the drug–side effect pairs.

We think that this database will make quite a bit of interesting research possible.

Negative controls and the police

Oh wow. In the last few years, the German police hunted a woman they only know from her DNA, which had been found at over 40 crime locations all over Germany and Austria (including the murder of a police officer in Heilbronn). Now, they slowly come to the conclusion that a charge of DNA collecting equipment got contaminated by a female employee... Running negative controls would have been really useful, no? (German source: stern.de, via: lawblog.de)