CMfinder

A tool to predict RNA motifs. It is an expectation maximization algorithm using covariance models for motif description, carefully crafted heuristics for effective motif search, and a novel Bayesian framework for structure prediction combining folding energy and sequence covariation. CMfinder performs well on unaligned sequences with long extraneous flanking regions, and in cases when the motif is only present in a subset of sequences. CMfinder also integrates directly with genome-scale homology search, and can be used for automatic refinement and expansion of RNA families.