TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure

Phylogenetic analysis and examination of protein domains allow accurate genome annotation and are invaluable to study proteins and protein complex evolution. However, two sequences can be homologous without sharing statistically significant amino acid or nucleotide identity, presenting a challenging bioinformatics problem. We present TreeDomViewer, a visualization tool available as a web-based interface that combines phylogenetic tree description, multiple sequence alignment and InterProScan data of sequences and generates a phylogenetic tree projecting the corresponding protein domain information onto the multiple sequence alignment. Thereby it makes use of existing domain prediction tools such as InterProScan. TreeDomViewer adopts an evolutionary perspective on how domain structure of two or more sequences can be aligned and compared, to subsequently infer the function of an unknown homolog. This provides insight into the function assignment of, in terms of amino acid substitution, very divergent but yet closely related family members. Our tool produces an interactive scalar vector graphics image that provides orthological relationship and domain content of proteins of interest at one glance. In addition, PDF, JPEG or PNG formatted output is also provided. These features make TreeDomViewer a valuable addition to the annotation pipeline of unknown genes or gene products. TreeDomViewer is available at

The 2009 framework for undergraduate medical education in the Netherlands

The 2009 Framework defines the joint Dutch national learning outcomes to be attained by medical students after completing their three-year master programme in medicine. The Framework thus helps to guarantee to society at large and to patients in particular that medical graduates who are starting out as practitioners have attained a certain professional level. This level is the aggregate of the physicians’ target profile, physicians’ (sub-) competencies to be achieved and the list of issues relating to illness and health. In addition, the Framework also defines the profile of the bachelor and the learning outcomes of the bachelor programme in medicine

The 2009 framework for undergraduate medical education in the Netherlands

The 2009 Framework defines the joint Dutch national learning outcomes to be attained by medical students after completing their three-year master programme in medicine. The Framework thus helps to guarantee to society at large and to patients in particular that medical graduates who are starting out as practitioners have attained a certain professional level. This level is the aggregate of the physicians’ target profile, physicians’ (sub-) competencies to be achieved and the list of issues relating to illness and health. In addition, the Framework also defines the profile of the bachelor and the learning outcomes of the bachelor programme in medicine

Controlling the temperature sensitivity of DNA-mediated colloidal interactions through competing linkages

We propose a new strategy to improve the self-assembly properties of DNA-functionalised colloids. The problem that we address is that DNA-functionalised colloids typically crystallize in a narrow temperature window, if at all. The underlying reason is the extreme sensitivity of DNA-mediated interactions to temperature or other physical control parameters. We propose to widen the window for colloidal crystallization by exploiting the competition between DNA linkages with different nucleotide sequences, which results in a temperature-dependent switching of the dominant bond type. Following such a strategy, we can decrease the temperature dependence of DNA-mediated self assembly to make systems that can crystallize in a wider temperature window than is possible with existing systems of DNA functionalised colloids. We report Monte Carlo simulations that show that the proposed strategy can indeed work in practice for real systems and specific, designable DNA sequences. Depending on the length ratio of the different DNA constructs, we find that the bond switching is either energetically driven (equal length or `symmetric' DNA) or controlled by a combinatorial entropy gain (`asymmetric' DNA), which results from the large number of possible binding partners for each DNA strand. We provide specific suggestions for the DNA sequences with which these effects can be achieved experimentally

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.

doi:10.1093/nar/gkn23

ProGMap: an integrated annotation resource for protein orthology

Current protein sequence databases employ different classification schemes that often provide conflicting annotations, especially for poorly characterized proteins. ProGMap (Protein Group Mappings, http://www.bioinformatics.nl/progmap) is a web-tool designed to help researchers and database annotators to assess the coherence of protein groups defined in various databases and thereby facilitate the annotation of newly sequenced proteins. ProGMap is based on a non-redundant dataset of over 6.6 million protein sequences which is mapped to 240 000 protein group descriptions collected from UniProt, RefSeq, Ensembl, COG, KOG, OrthoMCL-DB, HomoloGene, TRIBES and PIRSF. ProGMap combines the underlying classification schemes via a network of links constructed by a fast and fully automated mapping approach originally developed for document classification. The web interface enables queries to be made using sequence identifiers, gene symbols, protein functions or amino acid and nucleotide sequences. For the latter query type BLAST similarity search and QuickMatch identity search services have been incorporated, for finding sequences similar (or identical) to a query sequence. ProGMap is meant to help users of high throughput methodologies who deal with partially annotated genomic data

Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks

Summary: Multi-netclust is a simple tool that allows users to extract connected clusters of data represented by different networks given in the form of matrices. The tool uses user-defined threshold values to combine the matrices, and uses a straightforward, memory-efficient graph algorithm to find clusters that are connected in all or in either of the networks. The tool is written in C/C++ and is available either as a form-based or as a command-line-based program running on Linux platforms. The algorithm is fast, processing a network of > 106 nodes and 108 edges takes only a few minutes on an ordinary computer

How many pennies for your pain? Willingness to compensate as a function of expected future interaction and intentionality feedback

Despite increased research efforts in the area of reconciliation and trust repair in economic relations, most studies depart from a victim’s perspective. Specifically, these studies evaluate the process of trust repair by looking at the impact of restoration tactics on victims’ reactions. We focused on the transgressor’s perspective and present findings from two studies that investigated how the amount of compensation that a transgressor is willing to pay depends on victims’ reactions to the transgression (i.e. whether they claim the transgression happened intentionally or unintentionally) and the time horizon of the relationship between the transgressor and the victim (future vs. no future interaction). We hypothesized and found that transgressors are willing to pay less compensation to a victim who believes the transgression happened intentionally (as opposed to unintentionally), but only so when they share no future interaction perspective together. When transgressors have a future interaction perspective with the victim, intentionality feedback does not affect compensation size

Радіолокаційно-вихрострумовий метод виявлення металів

Сучасний георадар – це складний геофізичний прилад для неруйнівного контролю неоднорідностей середовища. В основі роботи георадару лежить підповерхневе зондуванняявище відбивання електромагнітної хвилі від межі поділу шарів з різною діелектричною чи магнітною проникністю. Такими межами є локальні неоднорідності різної природи. Георадари з великою вірогідністю визначають цю неоднорідність та глибину її залягання, але не можуть визначити склад неоднорідності, наприклад, це сталь чи золото. Тому виникла необхідність у створенні георадару без цього недоліку