A protein storage file management system and method based on adaptive coding

Abstract

The present invention discloses a protein storage file management system and method based on adaptive coding, comprising an encoding record database, a decoding record database, an information encoding module, an information retrieval module, an information decoding module, and a result output module; the information encoding module is used to encode a file into an amino acid sequence; the information retrieval module is used to query the encoding and decoding records, and obtain the encoding file address based on the encoding record for subsequent decoding operations; the information decoding module is used to decode the amino acid sequence into a source file; and the result output module is used to output the results generated by the encoding and decoding. The protein storage file management system and method based on adaptive coding provided by the present invention realize a protein storage system with high storage density, low sequencing coverage, long storage time, high coupling degree, and strong plasticity, ensuring the security, reliability, and durability of data storage.

Description

Technical Field

[0001] The present invention relates to a protein storage file management system and method based on adaptive coding, belonging to the fields of computer and biology. Background Art

[0002] Proteins are macromolecular compounds composed of amino acids, characterized by high storage density, long storage life, and strong plasticity. Unlike traditional silicon-based media, protein storage and encoded information is written by using solid-phase peptide synthesis and protein ligation techniques to prepare polypeptide chains of a certain length. After synthesis, the polypeptide chains are stored as powders or incorporated into specific objects through physical doping or chemical cross-linking, achieving long-term, traceless, and stable storage of information. Artificially synthesized proteins are used to store text, images, audio, and other data. When needed, the polypeptide chains are sequenced using mass spectrometry sequencing technology. The sequenced fragments are then spliced ​​and decoded to regenerate the original data.

[0003] Protein encoding is a key technology in protein storage, directly impacting storage performance and data read / write integrity. Protein storage technology uses amino acid structural units as a carrier for information storage and encoding, boasting high storage density, long storage duration, high stability, and strong plasticity. Therefore, a protein storage file management method leveraging adaptive encoding is essential. Summary of the Invention

[0004] The purpose of the present invention is to achieve a protein storage technology with high storage density, low sequencing coverage, long storage time, high coupling degree and strong plasticity.

[0005] To achieve the above-mentioned object, a technical solution of the present invention is to provide a protein storage file management system based on adaptive coding. The protein storage file management system is a visual operation platform, characterized in that it includes an original file upload module, an information encoding module, an information decoding module, an encoding record database, a decoding record database, and a result output module, wherein:

[0006] The user calls the original file upload module through the control displayed on the web page to upload the original file;

[0007] The user calls the information encoding module through the control displayed on the web page, and the information encoding module encodes the original file uploaded by the original file uploading module into an amino acid sequence; if the encoding is successful, the information encoding module will feedback the encoding success information to the user through the web page, indicating that the encoding is completed; during the encoding process, the information encoding module accesses the encoding record database and saves the files and operation records generated during the information encoding process into the encoding record database;

[0008] The user invokes the information decoding module through the control displayed on the web page. The information decoding module sequences the protein polypeptide chain to obtain the amino acid fragment sequence, and decodes the amino acid fragment sequence into the original file based on the file and operation record generated during the information encoding process input by the user. The result output module feeds the original file output by the information decoding module back to the user through the web page. During the decoding process, the information decoding module accesses the decoding record database and saves the file and operation record generated during the information decoding process into the decoding record database.

[0009] The user calls the information retrieval module through the information retrieval page. After entering keywords on the information retrieval page, the information retrieval module obtains the keywords entered by the user, accesses the encoding record database or the decoding record database based on the keywords, and obtains the files and operation records generated in the matching information encoding process or information decoding process, and then feeds back to the user through the information retrieval page.

[0010] Preferably, the original file includes a text file, an image file or an audio file.

[0011] Preferably, the information encoding module adopts different encoding schemes for different encoding region positions and adopts a method of adaptively generating encoding constraint thresholds.

[0012] Preferably, the result output module exports the file to the local computer through the download function of the browser.

[0013] Another technical solution of the present invention is to provide a method for managing protein storage files with adaptive coding, characterized in that it includes the following steps:

[0014] S100, preprocessing: converting the original file into binary code;

[0015] S200, adding redundancy: using Reed-Solomon error correction code to add redundant information to the binary code generated in step S100;

[0016] S300, Segmentation: Segment the binary code after adding redundant information into n segments of equal length, add a numbered information sequence and an information sequence that enables random data access at both ends of each segment, and generate a random integer d based on the Robust Soliton distribution;

[0017] S400, adaptive coding:

[0018] According to the characteristics of the coding position, different coding methods are used for the two different situations of payload and non-payload in the code obtained in the previous step. The payload refers to the part of the code obtained in the previous step before redundancy is added, and the non-payload refers to the numbered information sequence added at both ends of each segment during segmentation and the information sequence that enables random data access;

[0019] S500, protein synthesis: synthesizing the amino acid sequence generated in step S400 into a polypeptide chain and preparing a protein information storage material;

[0020] S600, information decoding: restoring the amino acid sequence to the original file;

[0021] S700, result display: using the result output module to display the result of the original file generated in step S600 on the display screen, and save the result to the coding record database.

[0022] Preferably, in step S400, fountain code is used to encode the payload portion.

[0023] Preferably, in step S400, encoding the payload portion includes the following steps:

[0024] S401, Luby Transform: Based on the d value obtained in step S300, select d segments from the n segments and perform an XOR operation on them to generate a coding symbol. To ensure storage quality, a two-byte RS error correction code is introduced. The coding symbol and the error correction code are then combined into a droplet as the output of the Luby Transform.

[0025] S402, screening: First, the binary sequence of the droplet is converted into an amino acid sequence, and then the algorithm is used to screen the homopolymer and GC content of the droplet. If the droplet passes the screening, it is considered valid and added to the file for storage. If it fails the screening, it is considered invalid and deleted.

[0026] S403. Calculate constraint threshold: Adaptively calculate the GC content threshold for non-payload encoding based on the formula using the GC content of the payload encoding, so that the GC content is maintained at around 50% during protein synthesis and sequencing to achieve better results.

[0027] Preferably, in step S400, a constraint filtering strategy is adopted for encoding of the non-payload portion.

[0028] Preferably, in step S400, encoding the non-payload portion specifically includes the following steps:

[0029] S404, calculating characteristic values ​​such as GC content and continuity of the payload code set;

[0030] S405. Calculate and generate the GC content threshold and continuity threshold of the non-payload code set. Based on different storage conditions, storage content, experimental environments, and storage overhead, rationally select algorithms and constraints to ensure the encoding quality of the non-payload portion. Supported algorithms include the K-means multi-node optimizer (KMVO), the damped multi-node optimizer (DMVO), the dual-strategy Black Widow Optimizer (BMVO), and the Cauchy and Levy mutation strategy (CLGBO). Hamming distance constraints (Hamming) and memory edit distance constraints (Edit) are designed to reduce the similarity between amino acid sequences. Minimum free energy constraints (MFE) and melting temperature constraints (TM) are used to select amino acid sequences with greater thermal stability. Non-run length constraints (Non-run) can avoid consecutive identical amino acids, and GC constraints are used to constrain the GC content threshold of the non-payload code set. S406. Input the number of address bits required to encode the non-payload code set and determine whether the GC content threshold of the current non-payload code set exceeds the lower bound of the non-payload code set.

[0031] S407: If it exceeds, return to step S406; otherwise, go to step S408;

[0032] S408: Continue the next encoding process using the current non-payload encoding threshold.

[0033] Preferably, in step S600, the information decoding process includes the following steps:

[0034] First, the protein is amplified and sequenced by PCR, and error correction is performed using Reed-Solomon error correction code. Finally, redundant information in the amino acid sequence is removed and restored to the original file.

[0035] Compared with the prior art, the present invention has the following beneficial effects:

[0036] The present invention has a reasonable structural design and utilizes an adaptive coding technology. According to the characteristics of the coding position, different coding methods are adopted for two different situations: payload and non-payload. Original files in three formats, text, image, and audio, are encoded into protein storage materials with high storage density, low sequencing coverage, long storage time, high coupling degree, and strong plasticity, thereby ensuring the security, reliability, and durability of data storage. BRIEF DESCRIPTION OF THE DRAWINGS

[0037] Figure 1 This is the overall framework diagram of the protein storage file management system based on adaptive coding of the present invention;

[0038] Figure 2This is an overall framework diagram of the protein storage file management method based on adaptive coding of the present invention;

[0039] Figure 3 This is a binary code and amino acid mapping relationship diagram of the protein storage file management system based on adaptive coding of the present invention;

[0040] Figure 4 This is a flow chart of the information encoding module of the protein storage file management system based on adaptive coding of the present invention;

[0041] Figure 5 This is a flow chart of non-payload encoding in the information encoding module of the protein storage file management system based on adaptive encoding of the present invention;

[0042] Figure 6 This is a decoding flow chart of the protein storage file management system based on adaptive coding of the present invention. DETAILED DESCRIPTION

[0043] Below in conjunction with specific embodiment, further set forth the present invention.Should be understood that these embodiments are only used to illustrate the present invention and are not used in limiting the scope of the present invention.In addition, should be understood that after reading the content taught by the present invention, those skilled in the art can make various changes or modifications to the present invention, and these equivalent forms fall equally within the scope limited by the appended claims of the application.

[0044] like Figure 1 As shown, the embodiment of the present invention proposes a protein storage file management system based on adaptive coding. The protein storage file management system is a visual operation platform, including an original file upload module, an information encoding module, an information decoding module, an encoding record database, a decoding record database, and a result output module, wherein:

[0045] The user calls the original file upload module through the control displayed on the web page to upload the original file, which includes a text file, an image file or an audio file.

[0046] The user invokes the information encoding module via a control displayed on a webpage. The information encoding module then encodes the original file uploaded by the original file upload module into an amino acid sequence. If the encoding is successful, the information encoding module provides feedback to the user via the webpage, indicating the completion of the encoding process. During the encoding process, the information encoding module accesses a coding record database and saves the files and operation records generated during the encoding process.

[0047] The user invokes the information decoding module via a control displayed on a webpage. The module sequences the protein polypeptide chain to obtain an amino acid fragment sequence and decodes the amino acid fragment sequence into the original file based on the files and operation records generated during the information encoding process input by the user. The result output module returns the original file output by the information decoding module to the user via a webpage. During the decoding process, the information decoding module accesses a decoding record database and saves the files and operation records generated during the information decoding process.

[0048] The user calls the information retrieval module through the information retrieval page. After entering keywords on the information retrieval page, the information retrieval module obtains the keywords entered by the user, accesses the encoding record database or the decoding record database based on the keywords, and obtains the files and operation records generated in the matching information encoding process or information decoding process, and then feeds back to the user through the information retrieval page.

[0049] In this embodiment, the information encoding module adopts different encoding schemes for different coding region positions, and adopts a method of adaptively generating coding constraint thresholds to optimize at the system level to ensure efficient operation of each link, so that the synthesized protein has high storage density and low read coverage.

[0050] In this embodiment, the result output module exports the file to the local computer through the download function of the browser.

[0051] The following lists preferred embodiments of the protein storage file management system based on adaptive coding to clearly illustrate the content of the present invention. It should be clear that the content of the present invention is not limited to the following embodiments, and other improvements through conventional technical means of ordinary technicians in this field are also within the scope of the present invention.

[0052] like Figure 2 As shown, the embodiment of the present invention proposes an adaptively encoded protein storage file management method, comprising the following steps:

[0053] S100, pretreatment:

[0054] Before encoding the original file, it is necessary to convert it into a binary file and convert the original file into binary code. In this embodiment, files in the three formats of text, image, and audio can be selected as the original file.

[0055] S200, add redundancy:

[0056] Reed-Solomon (RS) error correction code is used to add redundant information to the binary code generated in step S100. By using the RS error correction code to add redundant information to the binary code, the storage error rate is reduced and the consistency of the information before and after storage is ensured.

[0057] S300, segmentation:

[0058] The binary code with redundant information added is divided into n segments of equal length. A numbered information sequence and an information sequence that can achieve random data access are added at both ends of each segment, and a random integer d is generated based on the Robust Soliton distribution.

[0059] S400, adaptive coding:

[0060] According to the characteristics of the encoding position, different encoding methods are used for the two different situations of payload and non-payload in the code obtained in the previous step. The payload refers to the part of the code obtained in the previous step before redundancy is added, and the non-payload refers to the numbered information sequence added at both ends of each segment during segmentation and the information sequence that enables random data access:

[0061] The payload is encoded using fountain code, which includes the following steps:

[0062] S401, Luby Transform: Based on the d value obtained in step S300, select d segments from the n segments and perform an XOR operation on them to generate a coding symbol. To ensure storage quality, a two-byte RS error correction code is introduced. The coding symbol and the error correction code are then combined into a droplet as the output of the Luby Transform.

[0063] S402, screening: First, the binary sequence of the droplet is converted into an amino acid sequence, and then the algorithm is used to screen the homopolymer and GC content of the droplet. If the droplet passes the screening, it is considered valid and added to the file for storage. If it fails the screening, it is considered invalid and deleted.

[0064] S403, calculate constraint threshold: adaptively calculate the GC content threshold of non-payload encoding according to the formula based on the GC content of the payload encoding, so that the GC content is maintained at around 50% during protein synthesis and sequencing to obtain better results, such as Figure 4 As shown;

[0065] A constraint filtering strategy is used for encoding non-payload parts, and a variety of algorithms and combined constraints are available. The specific steps include:

[0066] S404, calculating characteristic values ​​such as GC content and continuity of the payload code set;

[0067] S405. Calculate and generate the GC content threshold and continuity threshold of the non-payload code set. Rationally select algorithms and constraints based on different storage conditions, storage content, experimental environments, and storage overhead to ensure the encoding quality of the non-payload portion. Supported algorithms include the K-means multi-node optimizer (KMVO), the damped multi-node optimizer (DMVO), the dual-strategy Black Widow Optimizer (BMVO), and the Cauchy and Levy mutation strategy (CLGBO). Hamming distance constraints (Hamming) and storage edit distance constraints (Edit) are designed to reduce the similarity between amino acid sequences. Minimum free energy constraints (MFE) and melting temperature constraints (TM) are used to select amino acid sequences with greater thermal stability. Non-run length constraints (Non-run) can avoid consecutive identical amino acids. GC constraints are used to constrain the GC content threshold of the non-payload code set.

[0068] S406: Input the number of address bits required to encode the non-payload code set, and determine whether the threshold condition of the current non-payload code set GC content exceeds the lower bound of the non-payload code set;

[0069] S407: If it exceeds, return to step S406; otherwise, go to step S408;

[0070] S408, continue the next encoding process using the current non-payload encoding threshold, such as Figure 5 shown.

[0071] S500, protein synthesis: synthesizing the amino acid sequence generated in step S400 into a polypeptide chain and preparing a protein information storage material.

[0072] S600, information decoding: restore the amino acid sequence to the original file, such as Figure 6 shown.

[0073] Specifically, the process of information decoding is the reverse process of information encoding. First, the protein needs to be PCR amplified and sequenced. To prevent errors during information reading, RS error correction code is used for error correction. Finally, redundant information in the amino acid sequence is removed and restored to the original file.

[0074] S700, result display: using the result output module to display the result of the original file generated in step S600 on the display screen, and save the result to the coding record database.

[0075] In summary, the present invention has the following advantages over the prior art:

[0076] The present invention utilizes an adaptive coding technology and adopts different coding methods for two different situations, namely payload and non-payload, according to the characteristics of the coding position. It encodes original files in three formats, namely text, image, and audio, into protein storage materials with high storage density, low sequencing coverage, long storage time, high coupling degree, and strong plasticity, thereby ensuring the security, reliability, and durability of data storage.

Claims

1. A method for managing protein storage files with adaptive coding, characterized in that: The steps include: S100, preprocessing: converting the original file into binary code; S200, adding redundancy: using Reed-Solomon error correction code to add redundant information to the binary code generated in step S100; S300, Segmentation: Segment the binary code after adding redundant information into n segments of equal length, add a numbered information sequence and an information sequence that enables random data access at both ends of each segment, and generate a random integer d based on the Robust Soliton distribution; S400, adaptive coding: According to the characteristics of the encoding position, different encoding methods are used for the two different situations of the payload and non-payload in the code obtained in the previous step. The payload refers to the part of the code obtained in the previous step before redundancy is added, and the non-payload refers to the numbered information sequence added at both ends of each segment during segmentation and the information sequence that enables random data access. The encoding of the payload part includes the following steps: S401, Luby Transform: Based on the d value obtained in step S300, select d segments from the n segments and perform an XOR operation on them to generate a coding symbol. To ensure storage quality, a two-byte RS error correction code is introduced. The coding symbol and the error correction code are then combined into a droplet as the output of the Luby Transform. S402, screening: First, the binary sequence of the droplet is converted into an amino acid sequence, and then the algorithm is used to screen the homopolymer and GC content of the droplet. If the droplet passes the screening, it is considered valid and added to the file for storage. If it fails the screening, it is considered invalid and deleted. S403. Calculate the constraint threshold: Adaptively calculate the GC content threshold for non-payload encoding based on the GC content of the payload encoding according to a formula, so that the GC content is maintained at 50% during protein synthesis and sequencing to achieve better results; The encoding of the non-payload part specifically includes the following steps: S404, calculating characteristic values ​​such as GC content and continuity of the payload code set; S405: Calculate and generate the threshold and continuity threshold of the GC content of the non-payload code set, and select algorithms and constraints based on different storage conditions, storage content, different experimental environments, and different storage costs; S406: Input the number of address bits required to encode the non-payload code set, and determine whether the threshold condition of the current non-payload code set GC content exceeds the lower bound of the non-payload code set; S407: If it exceeds, return to step S406; otherwise, go to step S408; S408: Continue the next encoding process using the current non-payload encoding threshold S500, protein synthesis: synthesizing the amino acid sequence generated in step S400 into a polypeptide chain and preparing a protein information storage material; S600, information decoding: restoring the amino acid sequence to the original file; S700, result display: using the result output module to display the result of the original file generated in step S600 on the display screen, and save the result to the coding record database.

2. The method for managing protein storage files with adaptive coding according to claim 1, wherein: In step S400, the payload portion is encoded using fountain code.

3. The method for managing protein storage files with adaptive coding according to claim 1, wherein: In step S400, a constraint filtering strategy is adopted for encoding of the non-payload portion.

4. The method for managing protein storage files with adaptive coding according to claim 1, wherein: In step S600, the information decoding process includes the following steps: First, the protein is amplified and sequenced by PCR, and error correction is performed using Reed-Solomon error correction code. Finally, redundant information in the amino acid sequence is removed and restored to the original file.

5. A protein storage file management system based on adaptive coding, which is a visual operating platform, adopts the protein storage file management method based on adaptive coding according to claim 1, characterized in that: It includes original file upload module, information encoding module, information decoding module, encoding record database, decoding record database, and result output module, among which: The user calls the original file upload module through the control displayed on the web page to upload the original file; The user calls the information encoding module through the control displayed on the web page, and the information encoding module encodes the original file uploaded by the original file uploading module into an amino acid sequence; if the encoding is successful, the information encoding module will feedback the encoding success information to the user through the web page, indicating that the encoding is completed; during the encoding process, the information encoding module accesses the encoding record database and saves the files and operation records generated during the information encoding process into the encoding record database; The user invokes the information decoding module through the control displayed on the web page. The information decoding module sequences the protein polypeptide chain to obtain the amino acid fragment sequence, and decodes the amino acid fragment sequence into the original file based on the file and operation record generated during the information encoding process input by the user. The result output module feeds the original file output by the information decoding module back to the user through the web page. During the decoding process, the information decoding module accesses the decoding record database and saves the file and operation record generated during the information decoding process into the decoding record database. The user calls the information retrieval module through the information retrieval page. After entering keywords on the information retrieval page, the information retrieval module obtains the keywords entered by the user, accesses the encoding record database or the decoding record database based on the keywords, and obtains the files and operation records generated in the matching information encoding process or information decoding process, and then feeds back to the user through the information retrieval page.

6. A protein storage file management system based on adaptive coding as claimed in claim 5, characterized in that: The original file includes a text file, an image file or an audio file.

7. A protein storage file management system based on adaptive coding as claimed in claim 5, characterized in that: The information coding module adopts different coding schemes for different coding area positions and adopts a method for adaptively generating coding constraint thresholds.

8. A protein storage file management system based on adaptive coding as claimed in claim 5, characterized in that: The result output module exports the file to the local computer through the download function of the browser.

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