Parallel Lara and RNA finding


  1. Devise computational methods for aligning (pseudoknotted) RNA families.
  2. Derive probabilistic global and local motifs from the alignments while allowing to incorporate experimental evidence.
  3. Search the motifs fast and sensitive in large genomic sequences.


The Lagrangian Relaxation Aligner (LaRA) aligns two or more RNA molecules with regard to their spatial structure. Hence, for each input sequence the program takes a base pair probability matrix (which can be obtained from ViennaRNA, for instance). The resulting alignment will later be used to analyze conserved structure motifs.

The LaRA program was re-implemented using the SeqAn library. Therefore, it benefits from very fast alignments and efficient data structures. The current version of SeqAn::LaRA can be examined here.