RNA secondary structure prediction is one of the most important fields in computational molecular biology.The method to predict RNA secondary structure is introduced

including the mathematic models

main algorithms and softwares.Then seven main softwares are tested and compared detailedly with some groups of tRNA and RNase P.It showed that Pfold performed better than others when several homologous RNA sequences were predicted.At last some vital aspects that may be conducted in the future investigations are discussed.