UNLABELLED Profile-based similarity search is an essential step in structure-function studies of proteins. However, inclusion of non-homologous sequence segments into a profile causes its corruption and results in false positives. Profile corruption is common in multidomain proteins, and single domains with long insertions are a significant source of errors. We developed a procedure (HangOut) t...

Summary: We present a software framework and tool called PIANA that facilitates working with protein interaction networks by 1) integrating data from multiple sources, 2) providing a library that handles graph-related tasks and 3) automating the analysis of proteinprotein interaction networks. PIANA can also be used as a standalone application to create protein interaction networks and perform ...

Distributed Constraint Optimization (DCOP) is a field that has recently been getting more and more attention from academia and industry. However, very few open-source, off-the-shelf tools are currently available to solve DCOPs; examples are FRODO, DisChoco and DCOPolis. A DCOP platform should possess the following key qualities: the framework should be reliable and extensively tested, deployabl...

We discover a pronounced dependence of the strength of the soft X-ray orbital modulation and the spectral hardness in Cyg X-1 in the hard state on its superorbital phase. We find our results can be well modelled as a combination of two effects: the precession of the accretion disc (which appears to cause the superorbital flux modulation) and the orbital-phase dependent X-ray absorption in an ac...

The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern p...

Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. However, the repeat nature of the tRNA templates and the idiosyncrasies of tRNA sequences necessitate the development and use of methodologies that differ markedly from those used to analy...