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README.md

RNAprob

A tool for data-directed RNA secondary structure prediction. It uses structure probing data to restrain structure prediction, and outputs MFE structure and suboptimal structures. It is based on RNAstructure package.

Citation

Fei Deng, Mirko Ledda, Sana Vaziri and Sharon Aviran. (2016). Data-directed RNA secondary structure prediction using probabilistic modeling. RNA, 22:1109–1119.

Installation

Users are required to choose the right compiler option based on the operation system used. It chooses Mac OS by default. To compile it on Linux, comment out lines from 33 to 36 and uncomment lines from 27 to 30. Similarly for Windows users.

First of all, enter the directory of RNAprob and type:

$ make RNAprob

The executable will then be placed in the directory RNAprob/exe. Note that you may need to change compiler setting in compiler.h based on your operating system. Then, specify the location of thermodynamic parameters and training parameters by adding the following line to .bashrc (create a .bashrc file if it does not exist on your computer):

export DATAPATH=[directory in which RNAprob resides]/data_tables/

Usage

Four variants of RNAprob are available, the general command is

$ RNAprob <seq file> <ct file> -sh <shape file> [options]
  • <seq file> : the name of a sequence file containing input sequence.

  • <ct file> : the name for output ct file.

  • <shape file> : the name of an input SHAPE profile.

Specifically, the commands to run each of the four variants of RNAprob are as follows:

  • RNAprob-3 : RNAprob <seq file> <ct file> -sh <shape file>

  • RNAprob-2 : RNAprob <seq file> <ct file> -sh <shape file> -2s

  • RNAprob-3s : RNAprob <seq file> <ct file> -sh <shape file> -smooth

  • RNAprob-2s : RNAprob <seq file> <ct file> -sh <shape file> -2s -smooth

scorer function

A scorer function that measures prediction accuracy of a predicted structure is also included. This function extends the scorer function provided in RNAstructure by adding the computation of Matthews Correlation Coefficient (MCC). To compile it, enter the directory of RNAprob and type:

$ make scorer

The executable will then be placed in the directory RNAprob/exe. The general command to run the scorer function is as follows:

$ scorer <predicted ct> <accepted ct> <output file> [options]

For more details, please refer to http://rna.urmc.rochester.edu/Text/scorer.html.

Licence

RNAprob is free for non-commercial research. For commercial use, please contact the authors.

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