I recently teamed up with a collegue to work together on a project because our individual research projects crossed paths. We devided work and each picked a gene family to work on. The resulting phylogenetic trees are depicted below.

Sometimes you can not beat good old fashioned paper .

I’m using Dendroscope as my prefered tree viewer, but I don’t know if there is anything better out there for viewing large phylogenies. If somebody can recomment me something, please drop me a comment!

Fortunately my wife shares my taste for Belgian beers and we are known to grade beers. Now, Westvleteren is a very special brewery in that it is one of the seven Trappist monastery breweries. But unlike the other six Westvleteren does not sell its beer through retail. In fact, you can only buy the beer at the monastery for your own consumption. The Westvleteren 12 is rated as one of the best beers in the world, which unfortunately does not work well for the monks. Anyway, I got one and I agree with the rest of the world. It is definitely my favorite!

I found this article in my email and at first sight it looked nice and useful to me, but I’m not even gonna try to read the article and try the software… Because I don’t have a Mac…

Should I get a Mac?

That analogy goes a long way!

I wanted to search a string using this regexp without knowing how many matches I would find:

$string =~ /\(\d+):/g

This would match ’15′  and ’20′ in a string which looks like this :

$string = "(yeast:0.12313,((zebrafish:0.12312,fugu:0.84134)15:0.52313,
human:0.94424)20:0.93313);";

One can access the found values by using backreferences (in this case $1 and $2). But what if you do not know how many backreferences there are?

This piece of perl code will return the values of all the backreferences:

my @array;
while ($string =~ /\)(\d+):/g) {
push @array, $1;
}

@array will contain the values of all the backreferences. Don’t ask me why this works…

van Dam, T.J.P., Snel, B. (2008). Protein Complex Evolution Does Not Involve Extensive Network Rewiring. PLoS Computational Biology, 4(7), e1000132. DOI: 10.1371/journal.pcbi.1000132

This is the author summary:

Protein complexes are a pivotal part of the functioning of cells in health and disease. Studying the evolution of these essential cellular features is of great intrinsic as well as practical interest. However, the study of the evolution of protein complexes by comparative analysis is fraught with difficulties. Hence current reports that reveal low overlap in the interactome between species are often reluctant to equate this low level of overlap to a low level of conservation. Here we exploit new public data sets, which display unparalleled coverage, to study the amount of co-complex membership conservation, and we present a novel measure for the absence of interactions. We thereby observe a hitherto unreported high level of conservation of 90% of the interactions when the presence of the genes coding for the protein pairs that participate in the same protein complex is also conserved. This allows for new insights into the evolution of protein complexes: the evolutionary dynamics of protein complexes are, by and large, not the result of network rewiring (i.e. acquisition or loss of co-complex memberships), but mainly due to genomic acquisition or loss of genes coding for subunits.

WordPress 2.6 provides a lot of new functionality though! Lets see how this Press This thing works…

Update: permalink structure works fine again! If you have the same problem check this. Option 2 worked fine for me!