STRMS is a tool for structural RNA motif search. The tool takes as input the secondary structure of the query and a target sequence database, and reports all occurrences of the query in the target. The tool takes into account a sequence and structure options. The search is based on subtree homeomorphism for ordered, rooted trees (which we use to represent the RNA structures) .
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Isana Veksler-Lublinsky, Michal Ziv-Ukelson, Danny Barash and Klara Kedem.
A Structure Based Flexible Search Method for ncRNA motifs.
Journal of Computational Biology 14(7): 908-926, 2007.