Inparablog

I have been racking my brains over this, but could not find help anywhere. It seems that doing wacky stuff in Perl out of desperation actually pays off!

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…

My very first article is out!

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.

I have just upgraded to WordPress 2.6. Unfortunately I have run into some trouble concerning the permalink structure of this site. Links such as http://www.myscience.nl/index.php/2007/07/08/eating-your-brainz/ will not work until it is fixed because I don’t have time to downgrade. Sorry…

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!

I thought I had them all, but I was wrong. When is something not sharing homology and when do you just fail to detect? I think this is still a big problem in bioinformatics… Bitscores or E-values? Which method? Blast, PSI-Blast, HMMER? Argggh!!!!

One of my colleagues showed me this. There are fungi which consume ants and other insects in order to spread their spores. The video below shows an ant infected by Cordyceps unilateralis which alters the behavior of the ant, forcing it to climb upwards ensuring effective spreading of spores. How cool is that!