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Compared to existing representations of H-type pseudoknots , the new representation ensures uniform and clear drawings with no edge crossing for all H-type pseudoknots . In the sense of graph theory , a drawing of RNA secondary structures is a tree , whereas a drawing of RNA pseudoknots is a graph with inner cycles within a pseudoknot as well as possible outer cycles formed between a pseudoknot and other structural elements . Note that this restricts the annotation to a maximum of 26 pseudoknots per sequence . Moreover , our algorithm can predict most types of potential pseudoknots in the RNA structure .