LaRA: Efficient sequence-structure alignments of ncRNA
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.
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
For questions, comments, or suggestions please contact: