tools
Posts tagged “tools”.
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.
Exploring the Lower Part of Discrete Polymer Model Energy Landscapes
This paper develops an efficient flooding-style algorithm for exploring the low-energy part of discrete polymer landscapes, making barrier-tree analysis feasible without exhaustive enumeration.