Research On The Algorithms Of RNA Sequence Alignment

Bioinformatics is a new science field. Research in this field involves multi-disciplines such as biology, computer science, mathematics, etc. RNA sequence alignment is the important topics of biological information, especially the RNA that contains the secondary and tertiary structure. Because the data of RNA sequence is massive, and the structure is very complex, so that sequence alignment is a time-consuming process, which is difficult to be proofed, the tertiary structure of RNA alignment is NP-hard problem. Improve the speed of sequence alignment, as well as the tertiary structure alignment, is the focus of this research.After the deep analysis of existing assembly methods and implementation softwares, we analyze the optimized algorithm of RNA secondary structure alignment by the tree-model. In addition, the paper discusses the difficulties of RNA tertiary structure alignment, and gives two tertiary structure alignment algorithms which base on the mapping of the secondary structure sequence, and transforming to the secondary structure, and analyze the result.Finally, the paper makes a deep analysis into the realization of improved algorithms and also presents some experiments of them. The testing results indicate that the algorithm of secondary structure alignment has a good time complexity, and that of the tertiary structure can tell the sequence similarity correctly, and it is related closely with the number of secondary structure. In the process of realization, consider about the characteristics of massive data, we put forward some optimization strategy, it includes memory optimization and dynamic programming retrospect optimization and it has a high processing efficiency.