https://github.com/tsudalab/mcts-rna
MCTS-RNA is a computational tool for solving RNA inverse folding problem with controlling the GC-content of the RNA sequence very precisely.
https://github.com/tsudalab/mcts-rna
monte-carlo-tree-search pseudoknot-structures rna
Last synced: 5 months ago
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MCTS-RNA is a computational tool for solving RNA inverse folding problem with controlling the GC-content of the RNA sequence very precisely.
- Host: GitHub
- URL: https://github.com/tsudalab/mcts-rna
- Owner: tsudalab
- Created: 2016-04-28T04:22:04.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2017-04-03T09:28:12.000Z (over 8 years ago)
- Last Synced: 2023-10-20T23:33:29.587Z (almost 2 years ago)
- Topics: monte-carlo-tree-search, pseudoknot-structures, rna
- Language: Python
- Size: 34.2 KB
- Stars: 9
- Watchers: 7
- Forks: 4
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# MCTS-RNA
MCTS-RNA is a tool for RNA inverse folding problem based on Monte Carlo Tree Search method. MCTS-RNA can design nested RNA structures and pseudoknot structures with user designed constraints: wide range and precise GC-content constraint and GC-content devation constraint.
# Requirements
1.RNAfold of [ViennaRNA Package](https://www.tbi.univie.ac.at/RNA/index.html) needs to be installed for designing nested structures.
2.[pKiss](http://bibiserv2.cebitec.uni-bielefeld.de/pkiss) is required for designing pseudoknot structures.
2.[Python](https://www.python.org/) required version is at least version 2.7.
3.Python library of [Numpy](http://www.numpy.org/) need to be installed.
# Installation
You can download the python script MCTS-RNA.py, run this script from the shell.
# How to use MCTS-RNA?
Once you downloaded the python script of MCTS-RNA and having installed all the requirements, you can execute MCTS-RNA from the shell. The inputs include the dot-bracket representation of target RNA secondary structure ,the target GC-content of the RNA sequence and GC-content error. The following are the examples and explanations of the inputs parameters.
This is an example of the command in the shell for nested RNA structures.
python MCTS-RNA.py -s "...(((((..........)))))........((((((((......))))))))(((((.......))))).............(((((..(((((..((..((.(((((.(((((.......))))).)))))...))....))))))))))))" -GC 0.75 -d 0.01 -pk 0
This is an example of the command in the shell for pseudoknot RNA structures.
python MCTS-RNA.py -s "....(((((.[[[[.))))).........]]]]..." -GC 0.4 -d 0.02 -pk 1
-s : The target RNA secondary structure.
-GC: The target GC-content of the RNA sequence, choose vaule from the range [0,1].
-d : The GC-content deviation of the solution, which is in range [0,0.02]. MCTS-RNA can output the sequence with more accurate GC-content with smaller GC-content devation setting, the default value of the GC-content devation is 0.01.
-pk: Design nested structure by setting -pk 0 and design pseudoknot structure by setting -pk 1 (currently MCTS-RNA only uses Pkiss) to predict pseudoknot structures.