Ben Gurion University of the Negev

Department of Computer Science

 

RNAfbinv: Fragment-Based Design of RNA sequences




RNAfbinv is an interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes. It is an extension of the RNAexinv inverse folding program that considers not only the secondary structure, the mutational robustness and the minimum free energy but also a motif constraint on the target RNA shape and a nucleotide constraint on the output sequence. The sequences that are generated may not fully conform to the given RNA secondary structure, but the nucleotide constraint and motif constraint are enforced, and the sequences strictly conform to 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.

RNAfbinv is the main application, two other applications that are relevant are RNAattributes and RNAfbinv-flex.

Operating System Architecture File Note
Linux x86 (64-bit)

 RNAfbinvGUI_Linux_64bit.tar.gz

Linux x86 (64-bit)

 RNAfbinvGUI_Extended_Linux_64bit.tar.gz

Extended version allows to start from a sequence
Linux x86 (32-bit)

 RNAfbinvGUI_Linux_32bit.tar.gz

Windows x86 (64-bit)

 RNAfbinvGUI_Windows_64bit.rar

Mac OS x86 (64-bit)

 RNAfbinvGUI_MacOs.tar.gz

- Extract the file with the commands:
1. >gunzip RNAfbinvGUI.tar.gz
2. >tar xvf RNAfbinvGUI.tar

More details on how to run RNAfbinv are available here.


Comments and inquiries should be sent to: dbarash@cs.bgu.ac.il