Rnall: RNA Local secondary structure prediction

Introduction

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.

License

Rnall was written by Xiu-Feng (Henry) Wan. The software Rnall is freely available for academic or non-commercial purpose at http://sysbio.cvm.msstate.edu/Rnall.

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 wan@cvm.msstate.edu.

Releases

NewCurrent Releases

Version 2.0 was jointly developed by Wan, X.-F., Lin, G., and Xu, D. Rnall scans the RNA sequence with a sliding window and extracts all LSS with sizes no longer than a window size using dynamic programming within a single run. Rnall has a time complexity of O(W3L) in the worse case, where W is the window size (typically a small constant less than 100 nt) and L is the sequence length. In practice, we observed an average computing time in O(W2L).

Windows Version

Linux Version

Release Achieves

Version 1.1 was jointly developed by Wan, X.-F. and Xu, D. 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 user manual 1.1 explains the installing and running commands for Rnall 1.1.

Documentation

The user manual 2.0 explains the installing and running commands for Rnall 2.0.

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