RNA Secondary Structure Alignment

• Main Authors: Meng-Yi Wu, 吳孟宜
• Other Authors: Chang-Biau Yang
• Format: Others
• Language: en_US
• Published: 2003
• Online Access: http://ndltd.ncl.edu.tw/handle/14631096118068722384

碩士 === 國立中山大學 === 資訊工程學系研究所 === 91 === The comparison methods for RNA or protein molecules are important basic tools in molecular biology. So far, most comparison methods are only applicable to the primary structures of biomolecules, such as the sequence alignment and comparison methods. The functions of biomolecules have close relationship with their structures. The recent methods for finding the structures of biomolecules are NMR spectroscopy, X-ray crystallography, and prediction with computational simulation. There are many biomolecules with known structures, but their functions are unknown. The RNA secondary structure alignment problem is to align two RNA molecules to get the structure similarity, where their secondary structures are given. In addition, it is also helpful to predict the functions of biomolecules and to classify them. In this thesis, we design a dynamic programming method for aligning two RNA secondary structures which do not contain any pseudoknot. The time complexity of our algorithm is O(N4), where N is the number of blocks contained in the given RNA sequences. We also apply our algorithm to the real biomolecules, the tRNAs of Homo sapiens mitochondrion, to evaluate the practicability our method. We take three tRNA genes, TRNG, TRNA and TRNV, to test the performance of our algorithm. From the view point of human eyes, in fact, the structure of TRNG is more similar to TRNA. Our algorithm also gets this result. Hence, our algorithm provides an effective method to measure the similarity of two RNA secondary structures.