new method
Posts tagged “new method”.
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...
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.
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.
Barrier trees: mapping minima, saddles and basins of energy landscapes
This paper develops the barrier-tree formalism for degenerate landscapes and helped establish a general language for analyzing basins, saddle points, and transition barriers in complex discrete systems.