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