RNAexinv ReadMe

Table of Contents


RNAexinv is an interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes. It is an extended inverse RNA folding program with the rationale behind that the generated sequences should not only fold into a desired structure, but they should also exhibit favorable attributes such as thermodynamic stability and mutational robustness. RNAexinv considers not only the secondary structure in order to design sequences, but also the mutational robustness and the minimum free energy. The sequences that are generated may not fully conform with the given RNA secondary structure, but they will strictly conform with the RNA shape of the given secondary structure and thereby take into consideration the recommended values of thermodynamic stability and mutational robustness that are provided.


You can download the package from : http://www.cs.bgu.ac.il/~RNAexinv


The Package Content

1. RNAexinv - this program performs all the calculations that are explained in the manuscript. The input to this program is the dot-bracket representation of the desired structure, the desired free energy in kcal/mol, and the desired neutrality value. The output of the program is the designed sequence. The package contains the executable and the source code that can be compiled by the make command.

2. Java code - this is a GUI that provides the interface for input parameters, running the RNAexinv program, and displaying the results in a table of designed sequences with the possibility to examine the drawings of the secondary structures.

Programs taken from the Vienna RNA package and used in the RNAexinv GUI:

1. RNAfold - predicts the minimum free energy secondary structures and base pairing probabilities.

2. RNAplot - draws the secondary structure of the RNA, given a sequence and the dot-bracket representation of the secondary structure.


Preparation and Compilation

RNAexinv can currently run only on a Linux platform. Therefore, all preparations and compilations that will be mentioned should be performed on a Linux platform with Java and "GNU CC" compiler installed. RNAexinv has all its components already compiled and may be used without any compilations as described in the "How to Run the Program" part, but it has some components written in C that in some architectures may not work. In such a case, the Vienna RNA package should be downloaded from the web at http://www.tbi.univie.ac.at/~ivo/RNA/ and compiled. After the compilation finishes, files: "RNAplot" and "RNAfold" should be copied from Vienna RNA to the "RNAexinvGUI\bin" directory. All files that are already in this directory should be overwritten. In order to compile RNAexinv, please go to the RNAexinvGUI\RNAexinv directory and run the make command. Copy the created RNAexinv executable to the RNAexinvGUI\bin directory.

Make sure that all files in the "RNAexinvGUI\bin" directory are in an executable mode. If not, change their mode by typing the command:  >chmod 700 file_name ,where file_name is each file from the \bin directory. At this point, the RNAexinvGUI utility can be used as described in the "How to Run the Program" part.



This program can currently run on a Linux platform only. For using this program, one needs to have "Java VM" installed on the computer.

For more information about downloading and installing Java click here.
Please make sure that the directory that contains the program and all subdirectories have the correct Read/Write permissions for all users working with this program.


How to Run the Program

Before running the program make sure that all the preparations are done.
Open a Unix shell, and go to the directory that contains the program (e.g. RNAexinvGUI).
The GUI for RNAexinv program can be started in the following way:

>java RunRNAexinv

The input screen that appears after running the command is shown in the following figure:

After pressing the "Result" button the following window will appear. These results are obtained from the same dot-bracket representation and parameters as appear in the input screen of the GUI.

The input dot-bracket representation and the input parameters are available at the top of the window, as well as the Shapiro representation of the same desired structure.

The rest of the window contains the found 20 sequences, ranked by their dot-bracket tree-edit distance relative to the wild-type predicted structure. Pressing on the button below each sequence will open the page with the information on this sequence.

For example, pressing on the button below the second sequence will open the following window:

The window contains:


End of ReadMe