The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de.

CRISPR–Cas systems are adaptive immune systems in prokaryotes, providing resistance against invading viruses and plasmids. The identification of CRISPR loci is currently a non-standardized, ambiguous process, requiring the manual combination of multiple tools, where existing tools detect only parts of the CRISPR-systems, and lack quality control, annotation and assessment capabilities of the detected CRISPR loci. Our CRISPRloci server provides the first resource for the prediction and assessment of all possible CRISPR loci. The server integrates a series of advanced Machine Learning tools within a seamless web interface featuring: (i) prediction of all CRISPR arrays in the correct orientation; (ii) definition of CRISPR leaders for each locus; and (iii) annotation of cas genes and their unambiguous classification. As a result, CRISPRloci is able to accurately determine the CRISPR array and associated information, such as: the Cas subtypes; cassette boundaries; accuracy of the repeat structure, orientation and leader sequence; virus-host interactions; self-targeting; as well as the annotation of cas genes, all of which have been missing from existing tools. This annotation is presented in an interactive interface, making it easy for scientists to gain an overview of the CRISPR system in their organism of interest. Predictions are also rendered in GFF format, enabling in-depth genome browser inspection. In summary, CRISPRloci constitutes a full suite for CRISPR–Cas system characterization that offers annotation quality previously available only after manual inspection.

The principles of protein folding and evolution pose problems of very high inherent complexity. Often these problems are tackled using simplified protein models, e.g. lattice proteins. The CPSP-tools package provides programs to solve exactly and completely the problems typical of studies using 3D lattice protein models. Among the tasks addressed are the prediction of (all) globally optimal and/or suboptimal structures as well as sequence design and neutral network exploration.

Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA’s 3D structure. Currently the design of RNA molecules, which fold into a specific structure (known as RNA inverse folding) within biotechnological applications, is lacking the feature of incorporating pseudoknot structures into the design. Hairpin-(H)- and kissing hairpin-(K)-type pseudoknots cover a wide range of biologically functional pseudoknots and can be represented on a secondary structure level. The RNA inverse folding program antaRNA, which takes secondary structure, target GC-content and sequence constraints as input, is extended to provide solutions for such H- and K-type pseudoknotted secondary structure constraint. We demonstrate the easy and flexible interchangeability of modules within the antaRNA framework by incorporating pKiss as structure prediction tool capable of predicting the mentioned pseudoknot types. The performance of the approach is demonstrated on a subset of the Pseudobase ++ dataset. This new service is available via a standalone version and is also part of the Freiburg RNA Tools webservice. Furthermore, antaRNA is available in Galaxy and is part of the RNA-workbench Docker image.

Research Highlights: Our results provide novel perspectives on the effectiveness and collapse of compensatory mechanisms of tracheid development of Norway spruce during intra-seasonal drought and the environmental control of intra-annual density fluctuations. Background and Objectives: This study aimed to compare and integrate complementary methods for investigating intra-annual wood formation dynamics to gain a better understanding of the endogenous and environmental control of tree-ring development and the impact of anticipated climatic changes on forest growth and productivity. Materials and Methods: We performed an integrated analysis of xylogenesis observations, quantitative wood anatomy, and point-dendrometer measurements of Norway spruce (Picea abies (L.) Karst.) trees growing along an elevational gradient in South-western Germany during a growing season with an anomalous dry June followed by an extraordinary humid July. Results: Strong endogenous control of tree-ring formation was suggested at the highest elevation where the decreasing rates of tracheid enlargement and wall thickening during drought were effectively compensated by increased cell differentiation duration. A shift to environmental control of tree-ring formation during drought was indicated at the lowest elevation, where we detected absence of compensatory mechanisms, eventually stimulating the formation of an intra-annual density fluctuation. Transient drought stress in June also led to bimodal patterns and decreasing daily rates of stem radial displacement, radial xylem growth, and woody biomass production. Comparing xylogenesis data with dendrometer measurements showed ambivalent results and it appears that, with decreasing daily rates of radial xylem growth, the signal-to-noise ratio in dendrometer time series between growth and fluctuations of tree water status becomes increasingly detrimental. Conclusions: Our study provides new perspectives into the complex interplay between rates and durations of tracheid development during dry-wet cycles, and, thereby, contributes to an improved and mechanistic understanding of the environmental control of wood formation processes, leading to the formation of intra-annual density fluctuations in tree-rings of Norway spruce.

Chemical reactions are rearrangements of chemical bonds. Each atom in an educt molecule thus appears again in a specific position of one of the reaction products. This bijection between educt and product atoms is not reported by chemical reaction databases, however, so that the “Atom Mapping Problem” of finding this bijection is left as an important computational task for many practical applications in computational chemistry and systems biology. Elementary chemical reactions feature a cyclic imaginary transition state (ITS) that imposes additional restrictions on the bijection between educt and product atoms that are not taken into account by previous approaches. We demonstrate that Constraint Programming is well-suited to solving the Atom Mapping Problem in this setting. The performance of our approach is evaluated for a manually curated subset of chemical reactions from the KEGG database featuring various ITS cycle layouts and reaction mechanisms.