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The Research on Prediction of RNA Secondary Structure

Author: WangJinHua
Tutor: LuoZhiGang
School: National University of Defense Science and Technology
Course: Software Engineering
Keywords: RNA secondary structure prediction Partition function Maximum expected accuracy rate Covariance Iterative
CLC: Q75
Type: Master's thesis
Year: 2007
Downloads: 119
Quote: 1
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Abstract

The biological function of the molecule and its structure is closely related to, even in a completely different species, the same functional molecules exhibit very similar structures. For RNA molecule, on the one hand, due to its secondary structure constitutes the tertiary structure, or even quaternary structure of main skeleton contains molecules folded state most of the free energy, so that RNA secondary structure can be partially or fully explain RNA The function of the molecule. The other hand, since the RNA molecules having a degradation of speed, and difficult crystallization, making the test method the three-dimensional structure of the RNA molecules spend a high cost and a long time. Therefore, through the use of computer tools and mathematical methods from the theoretically predicted secondary structure of RNA molecules, thus revealing the function of RNA molecules is very necessary. This article consists of the content and results of the following three parts: The first part describes RNA secondary structure prediction methods, their scope of application, as well as their advantages and disadvantages. Due to the conservative nature of the of homologous RNA molecule structure, so when there are multiple homologous RNA sequences, comparative sequence analysis method is an effective means of RNA secondary structure prediction. When only one or very few RNA sequence, comparative sequence analysis is no longer applicable, the minimum free energy method is used. To realize the advantages of both, more and more algorithm is both combined prediction structure. The second part, the use of RNA molecules to form various possible when the energy distribution of the secondary structure to predict the feasibility of a secondary structure of the RNA sequence. First introduced in detail the concept and calculation of the partition function and base pairing probabilities of RNA molecules. And then based on the correct definition of the maximum expected to discuss how to use the base pairing probability matrix to predict the secondary structure of RNA molecules, and it has a maximum expected accuracy rate. Finally, select the number of sequences tested it with the minimum free energy algorithm RNAfold compared. The preliminary results show that the prediction accuracy rate is usually slightly higher than RNAfold. The third part of the study of how comprehensive the minimum free energy and covariance the predicted homologous RNA sequences common secondary structure of the method and iterative thinking in the application of predicted pseudoknots. First of homologous RNA sequences average minimum free energy formula and the covariant score both combined. And then discuss the predicted pseudo-knot capability iterative thinking, and on this basis, based on the average minimum free energy and covariant information to predict the iterative method of homologous RNA sequences Public secondary structure. Finally, testing and comparative analysis. The results show that it has some advantages compared with other methods, because the prediction results after simple treatment, its sensitivity and specificity are close to or reach the optimal.

The Research on Prediction of RNA Secondary Structure

Abstract

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