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Scarna
Stem Candidate Aligner for RNA (Scarna) is a tool for sequence analyses of RNAs. It aligns two RNA sequences and calculates the similarities of them, based on the estimated common secondary structures. Scarna is a fast, convenient tool for clustering RNA sequences and for similarity search in long sequences. It works even for pseudoknotted secondary structures.
Publication
Yasuo Tabei, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai:"SCARNA:Fast and Accurate Structural Alignment of RNA Sequences by Matching Fixed-length Stem Fragments," Bioinformatics Advance Access published on May 11, 2006. doi:10.1093/bioinformatics/btl182