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).
Systems Biology Laboratory, College of Veterinary Medicine,Mississippi State University
- Windows / Linux
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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.