The present invention is intended to provide a kind of prediction RNA secondary structures thus RNA secondary structures, the secondary structure hardly predicted be so far (for example, pseudonot structures), can be for prediction and for predicting RNA secondary structures, with this prediction technique. The above method predicts RNA secondary structures, characterized by comprising: the base of the step constitute stem structure search can in subject's body RNA sequence; Stem structure is constituted based on each pedestal of free energy comprising steps of candidate stem structure is arranged; Determine the determining stem structure of step from stem structure candidate item; The stem structure that the search order state of the step is identified based on the master data of RNA sequence, as described above; The order energy of the step calculates each base and constitutes RNA sequence based on sequential organization state, as described above; RNA sequence secondary structure with the additional stem structure candidate of setting as newly identified stem structure based on sequence energy state, reflects the stem structure of identification, as described above,With the new secondary structure of sequence energy state, wherein the additional candidate stem structure of above-mentioned secondary structure reflection is selected from above-mentioned stem structure candidate.
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