locarna

LocARNA provides several tools for the structural analysis of RNA

LocARNA is a collection of alignment tools for the structural analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for analyzing sets of related RNAs without known common structure. LocARNA distinguishes itself from many other Sankoff-style multiple alignment programs by its performance and low memory complexity, high accuracy, and richness of features. As unique features, it offers structure-local alignment, flexible structure and anchor constraints, and provides efficient computation of reliabilities in sequence-structure alignment. The package offers a robust core of features and is used as experimental platform for the incorporation of new features in RNA sequence-structure alignment.