Alignment of RNAs
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LocARNA: Alignment of RNAs

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.

At its core, the package offers global and local multiple alignment of RNAs.

Multiple alignment can be performed in one of several different ways:

  • progressive alignment using sequence-structure alignment of profiles

  • progressive alignment after consistency transformation using T-Coffee

  • progressive alignment using probabilistic consistency transformation and sequence-structure profile alignments, optionally followed by iterative refinement.

Besides of global alignment, LocARNA supports two kinds of locality. Local alignment as it is known from sequence alignment, identifies and aligns the best matching subsequences. This form of locality is called sequence local to distinguish it from structural locality. When performing structure local alignment, LocARNA identifies and aligns the best matching substructures in the RNAs. The sequences of those substructures can be discontinuous on the sequence level, but remain connected via structural bonds.

Alignment Reliabilities (LocARNA-P). In this special, probabilistic mode of operation LocARNA supports the efficient computation of match probabilities, probabilistic consistency transformation for more accurate multiple alignment, and generates reliability profiles of multiple alignments.


For installation on GNU/Linux and other Unix-like systems, please see file INSTALL.


For instructions on the use of the tools, please see the man pages of the tools

  • mlocarna --- for multiple alignment of RNAs. This program supports most of the functionality of the package via a high level interface.

  • locarnate --- for multiple alignment of RNAs via T-Coffee. This script offers multiple alignment of RNAs that is performed by sequence-structurally aligning all pairs of RNAs and then using T-Coffee to construct a common multiple alignment out of all pairwise ones.

and the low level tools for pairwise comparison of RNAs

  • locarna --- for pairwise alignment

  • locarna_p --- for pairwise computation of alignment partition function and (sequence and structure) match probabilities

Online information, download and web server

Further information is provided online at

The most recent versions of the package will be made available through this page.

The core functionality of the package is accessible through a web interface at


Main author and contact: Sebastian Will swill (at)