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).
Version 1.1 was jointly developed by Wan, X.-F. and Xu, D. It 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.