Welcome to the RNAmutants webserver !
This web server uses the software RNAmutants to compute, for each integer k, the minimum free energy structure MFE(k) and Boltzmann partition function Z(k) over all secondary structures of all k-point mutants of a given RNA sequence. In contrast to exhaustive enumeration, which is only possible for tiny sequences, RNAmutants uses dynamic programming to provide a complete analysis of the mutational landscape for a given RNA sequence. RNAmutants was implemented by Jerome Waldispühl, as described in
Jerome Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote.by extending an earlier algorithms of Waldispühl, Behzadi, Steyaert and Clote, Waldispühl, Behzadi and Steyaert to the Turner energy model. This computation is done simultaneously for all values of k ≤ Kmax, in time O(Kmax2*n3) with O(Kmax*n2) space requirements. See PLoS paper for mutational analysis of certain regulatory elements of human immunodeficiency and hepatitis C viruses. Further documentation is given in the manual.
Efficient algorithms for probing the RNA mutation landscape.
PLoS Comput Biol. 2008 Aug 8;4(8):e1000124.