Rnall V2.0 Manual

Rnall (RNA Local secondary structure prediction by Local symmetric mapping) version 2.0 is a new version RNA Local secondary structure prediction tool. Rnall 2.0 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. Different from Rnall 1.1, Rnall 2.0 extracts all LSS with sizes no longer than a window size. Furthermore, Rnall 2.0 incorporates thermodynamic parameters from the nearest neighbor model as the score function. 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).

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 Version 2.0 was jointly developed by Wan, X.-F., Lin, G., and Xu, D.
The software Rnall is freely available for academic or non-commercial purpose from HERE.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Any bug should refer to Xiu-Feng Wan by wan@sysbio.cvm.msstate.edu.

The current available version is Windows or Linux version.


Use any unzip software to extract the files


unzip the file:

gunzip Rnall.tar.Z
tar -xvf Rnall.tar

Running command:


Rnall2.0.exe -i filename -o outputfilename -g/-m [-w 50] [-l 10] [-e -5] -c


./Rnall2.0.exe -i filename -o outputfilename -g/-m [-w 50] [-l 10] [-e -5] -c
-i input file. the input file should be in the Fasta format
-o output file for predicted RNA local secondary structure
-g for scanning a single genome in the Fasta format
-m for multiple sequences in the Fasta format
-w for sliding window size (default 30)
-l for the lower window boundary for RNA LSS output (default =10, e.g. Rnall will output all of RNA LSS with size between 10 and 30 as default)
-e for energy threshold in the unit of Kcal/mol (default = -5)

Example1 for predicting RNA LSS energy landscape


Windows command:

Rnall2.0.exe -i test.fasta -o test.out -w 50 -l 30 -e 100 -g

Linux command:

./Rnall2.0.exe -i test.fasta -o test.out -w 50 -l 30 -e 100 -g

output: test.out

Example2 for outputting RNA LSS in CT format


Windows command:

Rnall2.0.exe -i test.fasta -o test.ct -w 50 -e -10 -g -c

Linux command:

./Rnall2.0.exe -i test.fasta -o test.ct -w 50 -e -10 -g -c

output: test.ct

Any usage of Rnall may cite the reference(s):

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.