RNHtool Files

Introduction:

1.	The RNHtool can be used to identify RNHs in retroviruses.
2.	The RNHtool was implemented in Microsoft Visual C++ 6.0 and supported on Windows environment. 
3.	The input and output files should be in FASTA format. RNH annotation clearly indicates the start and end positions of RNH in the inquired sequence.
4.	datasets:
  training-pol.fasta: pol sequences with RNH annotations for training.
  non-pol.fasta: non-pol (gag/env/pro..) sequences for scanning.
  pol.fasta: pol sequences without RNH annotations for scanning.
  np-RNHs.fasta: predicted np-RNHs after scanning the file of "pol.fasta".
5.	example:
1)	Please run the software named "RNHtool.exe".
2)	The screen shows a string of characters: "Please select an input file in FASTA format: ".
If the software and the input file are in the same folder, you can only type the name of the input file, such as: pol.fasta. If the software and the input file are not in the same folder, you should type the name and path of the input file, such as: E:\\dataset\\pol.fasta. The name and the path of the input file cannot contain a space.
3)	The screen shows a string of characters: "Please select an output file for predicted np-RNHs:".
If you want the output file and software in the same folder, you should only type the name of the output file, such as: "np-RNHs.fasta". If you want the output file in another folder, you should type the name and path of the output file, such as: "E:\\dataset\\np-RNHs.fasta". The name and the path of the output file cannot contain a space.
4)	Runining... 
Mission accomplished!
Then you can get the file containing the predicted np-RNHs.
5)	The screen shows a string of characters: "Do you want to input another file to predict np-RNHs? y/n".
Then you can input "y" to continue predicting np-RNHs, or "n" to quit the software.