UNLABELLED We present MetaRoute, an efficient search algorithm based on atom mapping rules and path weighting schemes that returns relevant or textbook-like routes between a source and a product metabolite within seconds for genome-scale networks. Its speed allows the algorithm to be used interactively through a web interface to visualize relevant routes and local networks for one or multiple o...

An 80-year-old man was admitted to our center because of recurrent ischemic strokes. Notably, the patient had recently been diagnosed with adenocarcinoma of the lung and was waiting to start radiation therapy. In addition, he was receiving chronic anticoagulation therapy with a coumarin derivative for permanent atrial fibrillation and maintained adequate international normalized ratio (INR) con...

1 Supplementary Experiments 1.1 Optimal Set of BirgRank Parameters To investigate how the four key parameters of BirgRank affect its prediction performance, we set each parameter as 0.1, 0.3, 0.5, 0.7 and 0.9, respectively, and test the prediction of protein functions using the yeast dataset with 50% of data as training set and the other 50% as testing set (missing function prediction, see the ...

UNLABELLED Mutational signatures are patterns in the occurrence of somatic single-nucleotide variants that can reflect underlying mutational processes. The SomaticSignatures package provides flexible, interoperable and easy-to-use tools that identify such signatures in cancer sequencing data. It facilitates large-scale, cross-dataset estimation of mutational signatures, implements existing meth...

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...

MOTIVATION Sequencing glycan structures is a difficult problem that requires the use of multiple experimental approaches. One powerful approach to glycan sequencing is the combination of liquid chromatography with sequential exoglycosidase digestions; however, interpreting this can be difficult and time-consuming. To aid this process, we introduce GlycoProfileAssigner, software for automated st...

UNLABELLED Here we present a computational protocol to analyze the promoter regions of a given set of co-expressed genes, and its implementation through the use of Web services technologies. This protocol aims to cluster a set of co-regulated genes in subsets of genes showing similar configurations of transcription factor binding sites. All the steps of this protocol have been developed as web ...

QCGWAS is an R package that automates the quality control of genome-wide association result files. Its main purpose is to facilitate the quality control of a large number of such files before meta-analysis. Alternatively, it can be used by individual cohorts to check their own result files. QCGWAS is flexible and has a wide range of options, allowing rapid generation of high-quality input files...

MOTIVATION To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies (RBs) in the fitted component. RESULTS Here we p...

Motivation Water molecules in protein binding sites play essential roles in biological processes. The popular 3D-RISM prediction method can calculate the solvent density distribution within minutes, but is difficult to convert it into explicit water molecules. Results We present GAsol, a tool that is capable of finding the network of water molecules that best fits a particular 3D-RISM density...