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 all LSS with sizes no longer than a window size using dynamic programming. Rnall has various potential applications, such as local secondary structure prediction in RNA molecules and RNA motif prediction (such as rho-independent/intrinsic terminator, riboswitch, siRNA, and viral RNA motifs).

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


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

System Requirements

Current versions of Rnall are available for both Windows and GNU/Linux system. If you need the versions for different operating systems, please contact Xiu-Feng (Henry) Wan by


If you have bug reports, questions, comments or suggestions, please contact Xiu-Feng (Henry) Wan by e-mail:

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. International Journal of Computer Science and Technology, 20: 465-482.