RNA inverse folding using ant-colony optimization
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Constraints
antarna
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README.md
plot_B_UB.py
setup.py

README.md

antaRNAdp - ant assembled RNA: Designing bistable RNA

Description

antaRNA is extended towards the usage of the ViennaRNA Tools python wrappers to get started with base pair probability matrices in order to calculate and model bistable RNA molecules and mimicking ligand interaction by applying constraints to simulate the induced conformation.

Usage

antaRNA can be used in several ways. This includes python object management or a direct command line call of the program. The program differentiates between two modi: MFE (dot-bracket structure optimization) and DP (dot plot structure optimization). Each of the modi has specific options and individual means of controlling its input. However, both modi also share options and input. Therefore a commandline call of the programm constitutes as:

$python antaRNA.py [COMMON INPUT AND OPTIONS] [MODUS{MFE,DP}] [MODUS INPUT AND OPTIONS]

See in Sources for detailed description of the explicit usage...

VERSION HISTORY OF antaRNAdp

  • v2.0.1

  • Bioconda Version

  • v2.0.0

  • new Terrain Graph and associated functions

  • new way of defining structural constraints

SOURCES

Algrithmic description and exemplary documentation

References

When using antaRNA in your work, please cite one of the following, suiting your work.