Unpaired Structural Entropy Calculation with Sliding Window


Unpaired Structural Entropy (USE) can be summarized as a simple objective function that was found to work well with miRNAs and other functional elements (e. g. intrinsic termination hairpin loops within the viral sequence).


USE utilizes NUPACK 2.1 to calculate the base pair and non pair probabilities. The user can access the webserver from the following link, there is a limit for running sequence of 10000nt in length with a maximum window size of 150nt. This restriction is to prevent the server from being overloaded. If -1 was inserted as the window size, USE will calculate the entire sequence for each fasta entry.


  • [Shaw et al, 2010] Shaw, T., Manzour, A., Wang, Y., Malmberg, R., and Cai, L. (2010) Analyzing modular RNA structure reveals low global structural entropy in microRNA sequences, Proceedings of Computational Systems Bioinformatics Conference (CSB2010), Vol. 9, p. 146-155.