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Tutorial like notebook to use salt option in RNAlib

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ViennaRNA/salty

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  • 'Salt Correction - Final Version.ipynb' is the jupyter notebook that produces all figures in the paper "Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package". The notebook also contains examples of using salt option in RNAlib. All figures are stored under "Fig/" directory. VARNAv3-93.jar is required if one wants to visualize the tRNA structure.
  • 'saltEnergy.py' is the python implementation for RNA salt correction, which is same as the one implemented in the ViennaRNA package.
  • 'create_ss.py' samples randomly and uniformly RNA sequences and folds them at different salt concentrations. The output MFE structures are stored under "ss/" directory. 'count_ss.py' counts the structural information of these MFE structures in "ss/" and summarized in 'ss_count_detail.csv',
  • 'download-dp-395.dp' contains the natural secondary structures featuring multiloop downloaded from the RNA STRAND database.
  • 'Data/' directory contains several experimental data that is used to compare with the model.

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Tutorial like notebook to use salt option in RNAlib

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