The present invention is to provide a method for predicting secondary structure of RNA capable of predicting the secondary structure which has been difficult to predict the secondary structure including pseudonot structure, and an apparatus for predicting secondary structure of RNA using the method for predicting. The method for predicting secondary structure of RNA according to the present invention is characterized in that:A method for predicting secondary structure of RNA comprising the steps of:searching base capable of forming a stem structure from the RNA sequence to be predicted;arranging a candidate stem structure based on a free energy of each base constituting said stem structure;arranging a defined stem structure from said candidate stem structure;investigating a sequence structure state of said RNA sequence based on the basic information of said defined stem structure;calculating a sequence energy state of each base constituting said RNA sequence based on said sequence structure state; andarranging a candidate additional stem structure as a new defined stem structure based on a sequence energy state of the secondary structure of said RNA sequence as reflected with said defined stem structure and on a sequence energy state of a new secondary structure as reflected on said secondary structure with the candidate additional stem structure selected from said candidate stem structure.
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