Beyond Pango: The future of virus lineage classification
Keeping pace with ever-changing viruses is a challenge. This study unveils an automated system for classifying viral lineages based on genetics, offering a faster and more objective approach
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SHAPE directed RNA folding with the ViennaRNA Package
The ViennaRNA Package 2.0 brings powerful dynamic programming algorithms to researchers studying nucleic acid folding. In this post, we explore three SHAPE-guided methods—Deigan, Zarringhalam, and Washietl—that have been integrated into our toolkit to improve predictions of base pair interactions and minimum free energy (MFE) structures for RNA molecules. By combining chemical probing data with in silico modeling, these approaches help capture real-world folding behaviors and enhance the accuracy of computational RNA structure predictions
Building efficient NGS analysis pipelines with ViennaNGS
ViennaNGS is a workflow system for building efficient NGS data analysis pipelines, integrating high-level routines and wrapper functions for common NGS processing tasks
How to efficiently explore the lower portion of RNA energy landscapes
Discrete energy landscapes provide a valuable means for analyzing non-equilibrium properties of biopolymers. In this study we propose a memory-efficient approach for local flooding of the lower portion of an RNA folding landscape
Bacterial transcription start site annotation from dRNA-seq data
A RESTful web service and standalone application for automated de-novo annotation of bacterial transcription start sites from dRNA-seq data
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