Rnall V1.1 Release Information


Rnall (RNA Local secondary structure prediction by Local symmetric mapping) predicts local RNA secondary structures for multiple sequences in the Fasta format or scans local secondary structure of a single genomic sequence in the Fasta format. Rnall scans the RNA sequence with a sliding window and extracts local secondary structure candidates based on dynamic programming. Then Rnall uses thermodynamic energy parameters to calculate the energies of local secondary structures. Rnall has various potential applications, such as local secondary structure prediction in RNA molecules, rho-independent terminator prediction, RNA motif prediction, and mi-RNA precursor prediction.

Rnall is written in C/C++, and is available for GNU/Linux at the present time.


Rnall was written by Xiu-Feng (Henry) Wan.The software Rnall is freely available for academic or non-commercial purpose from HERE.

System Requirements

Current versions of Rnall are only available for GNU/Linux system. If you need the versions for different operating systems, please contact Xiu-Feng (Henry) Wan by e-mail: wan@cvm.msstate.edu.


Version 1.1 is a general RNA local secondary structure prediction tool as well as a tool for intrinsic terminator (rho-independent terminator) prediction.


The newer version Rnall 2.0 is also available.


The user manual v1.1 explains the installing and running commands for Rnall.

Contact Address

If you have bug reports, questions, comments or suggestions, please contact Xiu-Feng (Henry) Wan by e-mail: wan@cvm.msstate.edu.

If you wish to acknowledge the use of Rnall in a publication, you should cite:
  • Wan, X.-F., G. Lin, and D. Xu. 2006. Rnall: An efficient algorithm for predicting RNA local secondary structural landscape in genomes. Journal of Bioinformatics and Computational Biology, 4(5):1015-31.

  • Wan, X.-F. and D. Xu. 2005. Intrinsic terminator prediction and its application in Synechococcus sp. WH8102. Journal of Computer Science and Technology, 20: 465-482.