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Pseudoknot-carrying nucleic acid structure prediction method based on multi-target genetic algorithm

A multi-target genetic and predictive technology, applied in the analysis of two-dimensional or three-dimensional molecular structures, instruments, biostatistics, etc., can solve the problems of ineffective RNA sequences, high time and space complexity, and reduce Time complexity and space complexity, the effect of improving accuracy and reducing forecast cost

Active Publication Date: 2019-04-09
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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  • Pseudoknot-carrying nucleic acid structure prediction method based on multi-target genetic algorithm
  • Pseudoknot-carrying nucleic acid structure prediction method based on multi-target genetic algorithm
  • Pseudoknot-carrying nucleic acid structure prediction method based on multi-target genetic algorithm

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Embodiment Construction

[0044] In order to make the present invention easier to understand, the technical solutions of the present invention will be further described below in conjunction with the accompanying drawings and embodiments.

[0045] Such as image 3 Shown, a kind of embodiment of the band pseudoknot nucleic acid structure prediction method based on multi-objective genetic algorithm of the present invention, comprises the following steps:

[0046] S100, set the minimum number of stem regions MinStem, the minimum number of bases in the loop MinLoop, the maximum number of pseudoknots MaxPesudoKnot, the population size N, the mutation rate Pc, the crossover rate Pm, and the maximum evolutionary generation Gen to initialize.

[0047] As a preferred embodiment, in this example, 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 set to 3 by defaul...

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Abstract

The invention relates to a pseudoknot-carrying nucleic acid structure prediction method based on a multi-target genetic algorithm. The method comprises the following steps: determining a K continuousmatching set according to a minimum stem zone number and a minimum base number in cycles, generating an initial population, carrying out selection, crossover and variation on an RNA (Ribonucleic Acid)molecular sequence by using a multi-target genetic algorithm, carrying out nondominant sequencing and crowding distance sequencing so as to obtain an optimal solution set with a Pareto molecular structure, and finally selecting an RNA molecular structure with the minimum free energy from the optimal solution set as a final prediction result. By adopting the method, the time complexity and the space complexity are degraded, and the pseudoknot-carrying RNA molecular structure prediction accuracy is improved.

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 ribonucleic acid (hereinafter referred to as RNA), in particular to a method for predicting RNA based on a multi-objective genetic algorithm. Background technique [0002] The function of RNA sequences mainly depends on their three-dimensional structure, but it is very difficult to directly predict the corresponding spatial structure from the primary structure of RNA molecules. The secondary structure is formed by the pairing between bases in the primary structure and the self-folding of the polynucleotide chain, which not only includes sequence information, but also contains tertiary spatial structure information. Therefore, the prediction of RNA secondary structure through RNA primary structure has always been a hotspot in the study of RNA overall structure. [0003] Pseudoknots are the most extensive structural...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B15/00G16B40/00
Inventor 张凯许志伟吕育林胡威符海东张晓龙贺娟娟刘俊刘小明廖雪超
Owner WUHAN UNIV OF SCI & TECH
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