RNA-align is an algorithm for comparing 3D structures of RNA molecules. Starting from two RNA structures, RNA-align seeks optimal nucleotide-to-nucleotide alignments based on a heuristic dynamic programming iteration process, assisted by distance-based secondary structure assignments. The structural similarity of the selected alignment is assessed by a renormalized TM-score on the statistics of RNA structures in the PDB, where TM-scoreRNA has values in (0,1] with 1 indicating a perfect structure match and a score ≥0.45 corresponding to a structural similarity of the RNA pairs in the same Rfam family. RNA-align can also be used to compare double-stranded DNA structures.
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