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HARP is a heuristic algorithm for the pairwise alignment of none-restricted (arbitrary) class pseudoknotted RNA secondary structures. HARP is based on a novel graph representation and hashing of the graph's geodesic distances. HARP finds local similarities (local alignments) and combines them to larger common substructure.
HARP is highly-efficient in both time and memory: Alignment of pairs of the 23S ribosomal RNA (~2800 nucleotides) on Pentium4 1800 MHz processor with 1GB internal memory required on average less than a minute running time and 10 MB.
You can align your structures using HARP web application.