Stemloc

Stemloc is a program for pairwise RNA structural alignment based on probabilistic models of RNA structure known as Pair stochastic context-free grammars. Stemloc implements constrained versions of the Sankoff algorithms for simultaneous structure prediction and sequence alignment of multiple RNAs.

Stemloc can be downloaded as part of the DART software package. It accepts input files in either FASTA or Stockholm format.