DNA storage code optimization method employing barnacle algorithm based on weights and mixed mutation strategy

An optimization method and DNA sequence technology, applied in genomics, instrumentation, proteomics, etc., can solve the problems of inability to find new regions in the search stage, and the barnacle algorithm is easy to miss neighborhood solutions, achieving strong global search capabilities. , improve the average fitness, increase the effect of diversity

Pending Publication Date: 2022-02-18
DALIAN UNIV
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Problems solved by technology

[0004] In the existing DNA coding design method, the sequences are more and more concentrated around the parent sequence, and new regions cannot be found in the search stage, which is easy to fall into the limitation of local optimum; and the barnacle algorithm is easy to miss the neighborhood in the iterative process untie

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  • DNA storage code optimization method employing barnacle algorithm based on weights and mixed mutation strategy
  • DNA storage code optimization method employing barnacle algorithm based on weights and mixed mutation strategy
  • DNA storage code optimization method employing barnacle algorithm based on weights and mixed mutation strategy

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Embodiment 1

[0043] The embodiments of the present invention are implemented on the premise of the technical solutions of the present invention, and detailed implementation methods and specific operation processes are given, but the protection scope of the present invention is not limited to the following embodiments. In the example, the DNA coding length n is set to 6, the Hamming distance constraint is set to d≥4, and the full discontinuity constraint and GC content constraint are as described above.

[0044] Step 1: Initialize the required parameters, initial set and DNA code set of the barnacle algorithm based on weight and mixed mutation strategy;

[0045] Specifically, 500 DNA coding sequences with a length of 6 are generated initially. Initialize the relevant parameters required by the algorithm, such as the penis length pl is set to 7; firstly, use the constraints to screen 500 DNA coding sequences with a length of 6 to obtain the initial set. For this example, the simulation expe...

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Abstract

The invention discloses a DNA storage code optimization method employing barnacle algorithm based on weights and a mixed mutation strategy. The method specifically comprises the steps of: constructing an optimal DNA code sequence meeting a constraint condition, constructing a certain number of DNA sequences as an initial set, and carrying out evaluation and sorting on the fitness of the DNA sequences in the initial set; utilizing the obtained initial set, adopting the barnacle algorithm based on the weights and the mixed mutation strategy to perform continuous iterative search and optimization, thereby obtaining a DNA sequence with high fitness; judging whether the DNA sequence meets the constraint condition or not, and if the DNA sequence meets the constraint condition, adding the DNA sequence into a DNA code set; and finally, outputting an optimal DNA code set. According to the method, the DNA code set with a better number can be searched.

Description

technical field [0001] The invention belongs to the field of coding design in DNA storage, and specifically uses a weight-based position update rule and a mixed mutation strategy to improve the performance of a barnacle algorithm to optimize a DNA coding sequence. Background technique [0002] Digital information stored on floppy disks, optical and electronic media, and transmitted over the Internet fueled the next explosion of science, technology and art. However, the existing storage media is difficult to achieve large-capacity storage, and there are problems such as high maintenance costs, limited service life, and easy data loss. The storage industry is facing unprecedented opportunities and challenges. Looking for high-density, large-capacity, and long-term stable storage Medium is imminent. [0003] Since there is life on the earth, deoxyribose nucleic acid (DNA) molecules composed of four bases of adenine (A), thymine (T), guanine (G) and cytosine (C) store the infor...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B50/00G16B30/00G16B20/50
CPCG16B50/00G16B30/00G16B20/50
Inventor 王宾郑燕芬陈蓉蓉张强
Owner DALIAN UNIV
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