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Simulated annealing-based nucleic acid structure prediction method

A technology of simulated annealing and prediction methods, applied in the field of bioinformatics engineering, which can solve problems such as high time complexity and space complexity, and ineffective RNA sequences

Active Publication Date: 2019-01-25
WUHAN UNIV OF SCI & TECH
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Problems solved by technology

It can be seen that these prediction methods have high time complexity and space complexity, can only predict RNA secondary structures that strictly meet strict restrictions, and cannot be effective for long-chain RNA sequences

Method used

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  • Simulated annealing-based nucleic acid structure prediction method
  • Simulated annealing-based nucleic acid structure prediction method
  • Simulated annealing-based nucleic acid structure prediction method

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Embodiment Construction

[0060] In order to make the present invention easier to understand, the specific embodiments of the present invention will be further described below.

[0061] Such as image 3 Shown, a nucleic acid structure prediction method based on simulated annealing, comprising the following steps:

[0062] S100, set the minimum number of stem regions, the minimum number of bases in the ring, and the initial temperature value T 0 , critical temperature T 临 , molecular new state, molecular old state, the maximum number of pseudoknot cross-grouping; the minimum number of stem regions is set to 2, since the RNA sequence cannot be folded violently, there must be at least three bases in the loop, so the minimum number of bases in the loop needs to be The default setting is 3, the initial temperature value T 0 Can be set to 1500.

[0063] S101, denote the RNA sequence S as x 1 x 2 x 3 … x n , where x i ∈{A,C,G,U}, the length of the sequence is n, 1≤i≤j≤n; the length of the RNA sequenc...

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Abstract

The invention relates to a simulated annealing-based nucleic acid structure prediction method. According to the method, a random point matching list and consecutive matching numbers corresponding to each group of random points are determined on the basis of a minimum stem region number and an in-ring minimum base number; stem region candidates are generated; effective matching can be realized faster on the basis of the idea of simulated annealing; and an energy evaluation function is introduced to improve the accuracy of the prediction of RNA molecule pseudoknots; and therefore, time complexity and space complexity are decreased, and the accuracy of the prediction of the RNA molecule pseudoknots is improved. The invention is funded by the national natural science foundation of China (61472293).

Description

technical field [0001] The invention belongs to the field of biological information engineering, and relates to a method for predicting the secondary structure of RNA (ribonucleic acid), in particular to a method for predicting RNA pseudoknots based on a simulated annealing algorithm. Background technique [0002] The functions of RNA sequences mainly depend on their three-dimensional structures. Pseudoknots are the most extensive structural units in RNA sequences, and are very complex and stable RNA structures. Pseudoknots have structural, catalytic and regulatory functions in RNA sequences. Using data from X-ray diffraction and nuclear magnetic resonance (NMR), it is possible to deduce the 3D form of the function of long RNA strands. This method, while accurate, can only be carried out in an environment with relevant equipment, which is also very expensive and time-consuming. Therefore, methods using computer and thermodynamic models to predict the secondary structure of ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B15/10G16B15/00G16B40/00
Inventor 张凯吕育林张晓龙符海东胡威贺娟娟徐新刘小明刘俊朱子奇
Owner WUHAN UNIV OF SCI & TECH
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