Webserver to compute RNA hairpin Profile

If you find these programs helpful for your work, please cite the paper, Asymptotic number of hairpins of saturated RNA secondary structures by P. Clote, E. Kranakis and D. Krizanc, Bull Math Biol (2014).


C source code to compute minimum energy structure having k hairpins

Mathematica computations
These computations apply the theorems of Drmota-Lalley-Woods and of Drmota, in order to compute the number of structures and expected number of hairpins.
Python code using dynamic programming to compute expected number of hairpins

Hairpin analysis of STRAND database
Python programs to analyze the number of hairpins in the STRAND database (necessary, because the STRAND database does not compute the number of hairpins, although stack size, etc. is computed).
Hairpin analysis of Mathews' RNA collection: number of hairpins as function of RNA length