tools
Posts tagged “tools”.
RNAplfold tutorial: accessibility in long RNAs
How to compute the accessibility of a region with RNAplfold in the ViennaRNA Package, i.e. the probability that a stretch of nucleotides is unpaired, how to read the _lunp file, how to choose the...
ViennaRNA training and workshops for researchers, starting in 2027
A series of practical ViennaRNA training modules and workshops is in preparation at RNA Forecast, planned to begin in early 2027. The training is for researchers who use RNA structure prediction in their own work and...
Claude Code for data analysis with a cloud model and gpt-oss:20b on Ollama
How to get a reproducible analysis of a small CSV file out of Claude Code, once with a cloud model and once with gpt-oss:20b on a local Ollama server, and how to check the result independently of the agent. Both runs...
RNAfold tutorial: MFE, pair probabilities and ensemble output
How to read the output of RNAfold in the ViennaRNA Package, i.e. the minimum free energy structure, the pair probabilities, the centroid and MEA structures, the suboptimal structures from RNAsubopt, and how to tell...
SHAPE and chemical probing tutorial: folding with reactivities in RNAfold
How SHAPE reactivities go into RNAfold, what the three methods in ViennaRNA do with them, and what probing data change in a prediction and what they do not. Worked example with yeast tRNA-Phe, all commands included.