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Predict RNA secondary structure calculation method

Author: LiuZhenDong
Tutor: ZhuDaMing
School: Shandong University
Course: Computer Software and Theory
Keywords: RNA secondary structure Pseudo - node Dynamic Programming Thermokinetic Stacked
CLC: TP301.6
Type: Master's thesis
Year: 2005
Downloads: 123
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Abstract

DNA is the carrier of genetic information, the role of genetic information is usually by the function of the protein to the performance, but the DNA is not a direct template for protein synthesis, protein synthesis template is RNA. RNA secondary structure prediction problem is one of the fundamental issues in computer science and bioinformatics, RNA secondary structure prediction for protein function analysis, sequence comparison analysis and thermal dynamics of minimum free energy method is two RNA secondary structure prediction basic ways, the sequence of comparative analysis of the basic idea is to find the similarity of the detection sequence and the target sequence. Sequence comparison is eventually achieved, must rely on a mathematical model, in the case of the sequence is very similar or new independent sequences, sequence comparison method is suited. At present, the the thermokinetic minimum free energy method has become the most commonly used method for RNA secondary structure prediction. Currently, most of the RNA secondary structure prediction algorithms only forecast nested RNA secondary structure does not allow pseudo-node exists. However, the pseudo-node has an important function in several known RNA. If Pleij et al 1985 predicted pseudo-node structure RnaSe P RNAS, by Kock and others to be confirmed in 1998. Contains pseudo-node RNA secondary structure prediction problem is the problem of NPC. Predict RNA secondary structure contains pseudo-node dynamic programming algorithms: of Rivals the algorithm, B.Lyngsφ algorithms and Jens Reeder algebraic dynamic programming algorithm. Rivals the algorithm, B.Lyngsφ algorithm can predict RNA secondary structure contains a pseudo-node the Rivas, algorithm calculates contains any plane pseudo node and specific conditions of the non-planar pseudo-node structure, its time complexity is O (n 6), the space complexity is O (n ~ 4). The only computable structure contains a flat pseudo node Lyngsφ algorithm time complexity of O (n ~ 5), space complexity is O (n ~ 3). Recently, a better prediction algorithm uses its O (n ~ 4) time and O (n ~ 3) of spatial prediction pseudo node arbitrary plane. Dynamic programming algorithm requires time and space, the predicted length greater than 1000 bases of RNA secondary structure is very difficult. The secondary structure of nested algorithm can not predict the pseudo-node structure, therefore an urgent need for a fast algorithm to predict RNA secondary structure contains pseudo-node. In this paper, a predicted RNA secondary structure of the greedy algorithm, the algorithm thought for RNA secondary structure calculation has stacked up, the idea comes from the \

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