LaRA: Efficient sequence-structure alignments of ncRNA

General context

The function of non-coding RNA sequences is largely determined by their spatial conformation, formed by Watson-Crick interactions between nucleotides. In order to discover yet unknown RNA families and infer their possible functions, the structural alignment of RNAs is an essential task, which demands a lot of computational resources and efficient algorithms. Some secondary structures contain overlapping interactions (called pseudoknots), which add additional complexity to the problem and are often ignored in available software.

Tool description

LaRA (Lagrangian Relaxed structural Alignments) is a tool for computing pairwise sequence-structure alignments and can be extended with T-Coffee or MAFFT in order to compute structural alignments of more than two structured RNA sequences. It is significantly faster than comparable software for accurate structural alignments due to its efficient implementation that uses multi-threading and SIMD vectorization. In contrast to other programs our approach handles arbitrary pseudoknots.
LaRA employs methods from combinatorial optimization to compute feasible solutions for an integer linear program. The optimization process is iterative and the advantage is that it can terminate as soon as the desired precision is reached.

input: sequence file with two or more sequences, optional with structure annotation
output: pairwise structural alignments in library format for T-Coffee or a fasta-like format for MAFFT

Links

For further information as well as setup and usage instructions please visit the LaRA homepage: 

Contact

For questions, comments, or suggestions please contact:

Jörg Winkler
j.winkler@fu-berlin.de