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We propose a novel representation of RNA secondary structure for a quick comparison of different structures. Secondary structure was viewed as a set of stems and each stem was represented by two values according to its position. Using this representation, we improved the comparative sequence analysis method results and the minimum free-energy model. In the comparative sequence analysis method, a novel algorithm independent of multiple sequence alignment was developed to improve performance.doi:10.4238/vol10-3gmr1181 pmid:21948761 fatcat:fzy7xe3gpvd77pps32sariuvdi