tools
Posts tagged “tools”.
SHAPE-directed RNA folding with ViennaRNA: reactivities as soft constraints
This paper shows how SHAPE-guided RNA folding is implemented in the ViennaRNA Package, comparing three widely used strategies for turning nucleotide reactivities into soft constraints that improve thermodynamic...
Building efficient NGS analysis pipelines with ViennaNGS
ViennaNGS is a modular toolbox for building reproducible NGS analysis workflows, combining Perl library code, utility scripts, and browser-oriented data-export components for early high-throughput genomics pipelines.
Memory-efficient exploration of RNA energy landscapes
This paper revisits the earlier flooding-based landscape methods and adapts them to RNA secondary structures with a local, memory-efficient enumeration strategy.
Bacterial transcription start site annotation from dRNA-seq data
TSSAR introduced statistically grounded, automated annotation of bacterial transcription start sites from dRNA-seq data and packaged it as both a RESTful web service and a standalone tool.
Visualization of lattice-based protein folding simulations
This conference paper presents visualization strategies for lattice-based protein folding simulations, turning complex folding trajectories and energy-landscape transitions into interpretable interactive representations.