History

J. Waldispühl, B. Behzadi and J.-M. Steyaert developed and implemented the general approximation grammar for multi-tape S-attribute grammars, which is described in [1]. Later these authors developed the application of AMSAG to compute k-superoptimal secondary structures.

P. Clote developed and implemented the dynamic programming algorithm in Python to computer the Boltzmann partition function Zk for all secondary structures of all k-point mutants of a given RNA sequence length n, where 0 ≤ k ≤ n. The partition function then yields the expected energy of all secondary structures of all k-point mutants, which equals RT2 times the partial derivative of the logarithm of the partition function Zk with respect to absolute temperature T.

Tony Schreiner translated the Python code of P. Clote into C.

Bibliography

  1. Waldispühl J, Behzadi B, Steyaert JM.
    An approximate matching algorithm for finding (sub-)optimal sequences in S-attributed grammars.
    Bioinformatics 18 Suppl 2:S250-9 (2002).