The thesis mainly includes two sections of following contents and conclusions. ( 1) Based on stacking covariance and minimum free energy, the thesis presents an iteration algorithm to predict the consensus structure with pseudoknots of homology RNA sequences. 具体来讲,本文主要包括以下两部分的内容和结果:一、提出了一种基于堆积协变信息和最小自由能的同源RNA含伪结二级结构迭代预测算法。