98 results about "Dna storage" patented technology

The invention relates to the technical field of coding and decoding, and discloses a DNA storage coding and decoding method and device, electronic equipment and a storage medium, and the method comprises the steps: carrying out the information filling of to-be-coded data, and obtaining a target binary sequence; encoding and mapping the target binary sequence to obtain a DNA base sequence; identifying a coding error mode of the to-be-coded data according to the DNA base sequence; and according to the coding error mode, selecting a corresponding decoding algorithm to decode the DNA base sequence to obtain decoding data. Through the implementation of the invention, data conversion and information filling are performed on the to-be-coded data, so that the length of the to-be-coded data can meet the length requirement of the polarization code; the coding error mode corresponding to the DNA base sequence is identified for decoding, the decoding accuracy can be effectively improved through different coding error modes, and lossless compiling of the to-be-coded data is realized.

The invention discloses a semantic intelligent enhanced DNA storage method for the Internet of Things, and belongs to the crossing field of artificial intelligence and biological information storage, the compression efficiency and robustness of DNA image storage are effectively improved through introduced semantic extraction and a multi-read screening mechanism of design, key information areas in images are extracted through semantic extraction, and the compression efficiency and robustness of DNA image storage are improved. The method has the advantages that redundant backgrounds are eliminated, coding lengths are reduced, high-quality sequences are selected from sequencing copies by the aid of scoring and sequence analysis through a multi-read screening mechanism, fault tolerance is enhanced, the method is applicable to efficient semantic storage in scenes of the internet of things, the problem of low storage efficiency due to excessive redundant information in original images in existing DNA image storage methods is solved, and the method is applicable to high-efficiency semantic storage in scenes of the internet of things. And a high bit error rate exists in the DNA synthesis and sequencing process, so that the image recovery quality is influenced.

The invention discloses an information storage method based on DNA (deoxyribonucleic acid) coding, which comprises the following steps: converting digital information to be stored into a quaternary code, converting the quaternary code into a DNA sequence consisting of adenine A, cytosine C, guanine G and thymine T according to a preset mapping rule, and expressing an additional information dimension by using a chemical modification state of a nucleotide pair; inserting error detection and correction codes in the DNA sequence every a predetermined number of basic group positions, segmenting the encoded DNA sequence into a plurality of fragments with the length of 100-150bp, and adding a specific recognition sequence and an index marker at two ends of each fragment; a reversible thermosensitive response DNA nanostructure is used as a carrier, DNA fragments are selectively combined to the carrier, and hierarchical storage and rapid retrieval of information are realized through a temperature gradient control system; the DNA storage information density can be remarkably improved, the service life of DNA storage can be remarkably prolonged, and a novel technical path is provided for large-scale, long-term and safe molecular information storage.

The present application relates to the technical field of DNA storage. Provided are a method and apparatus for encryption and coding during DNA storage, and an electronic device and a storage medium. The method for encryption and coding comprises: acquiring data to be stored, and a first random number sequence and a second random number sequence which are generated by a hyperchaotic pseudo-random sequence generator; using the first random number sequence to encrypt the data to be stored, so as to obtain source data; performing DNA Raptor coding on the source data, and introducing the second random number sequence into a DNA Raptor coding process as a random number seed, so as to obtain at least one piece of coded data; and on the basis of a DNA base mapping rule, converting each piece of coded data into a corresponding DNA sequence, and generating a target DNA sequence from the DNA sequence corresponding to each piece of coded data. The present application solves the problem in the related art of data security being not taken into consideration during DNA storage.

The invention discloses a preserving fluid for stably preserving sample DNA at normal temperature and a preparation method thereof, and belongs to the technical field of biological sample preservation. The preserving fluid comprises a lysis system, a nucleic acid protection system and a buffering and stabilizing system, the cracking system comprises a composite surfactant and an enzymolysis auxiliary agent; the composite surface active agent is prepared from polyether polyol fatty acid ester and cocamidopropyl hydroxy sulfobetaine; the enzymolysis auxiliary agent comprises lysozyme Lyso-V and protease K; the nucleic acid protection system comprises a nitrogen heterocyclic polyamine-carboxylic acid derivative and dextran sulfate; the nitrogen heterocyclic polyamine-carboxylic acid derivative comprises 1, 4, 7, 10-tetraazacyclododecane-N, N ', N' ', N ''tetraacetic acid, 1, 4, 7-triazacyclononane-N, N', N''-triacetic acid, disodium ethylene diamine tetraacetate-nitrogen heterocyclic derivative, and diethylenetriamine pentaacetic acid-piperazine derivative, and the nitrogen heterocyclic polyamine-carboxylic acid derivative comprises 1, 4, 7, 10-tetraazacyclododecane-N, N ', N '', N'' tetraacetic acid, 1, 4, 7-triazacyclononane-N, N', N ''-triacetic acid. The buffering and stabilizing system comprises an amphoteric buffering agent and a polymer stabilizer; the amphoteric buffering agent comprises 2-(N-morpholino) ethanesulfonic acid and N-tri (hydroxymethyl) methylglycine.

The invention discloses a coding and decoding method and system based on DNA storage, electronic equipment and a storage medium. According to the scheme, original data is compressed into a binary sequence; grouping the binary sequence to obtain a plurality of groups of first subsequences; detecting the first subsequences, adding watermarks to the first subsequences meeting a preset type, and detecting first data types of all the first subsequences; executing corresponding coding operation on the first sub-sequence for the first data type to obtain a corresponding base sequence; synthesizing according to the obtained base sequence to obtain a target DNA sequence; original data can be obtained by decoding the target DNA sequence; the sequences are grouped and subjected to double-rule coding, so that the coding efficiency is improved, the GC content and the homopolymer length are limited, and the stability of DNA sequence synthesis is improved; the embodiment of the invention can be widely applied to the technical field of DNA storage.

The invention discloses a DNA sequence reconstruction method and system based on multi-scale attention and contrast learning, and relates to the technical field of DNA storage data reconstruction. Comprising the following steps: collecting a plurality of DNA sequence copies, screening out abnormal length sequences, and constructing a standardized clustering data set; performing one-hot coding and filling processing on the DNA sequence; extracting context dependent features and cross-sequence variation features; an Inter-Sequence multi-head attention mechanism is constructed to calculate the similarity between the sequences, and a weighted sequence tensor is generated; a global dependency relationship in the sequence is extracted through an Intra-Sequence multi-head attention mechanism; local offset features caused by insertion and deletion errors are extracted through a multi-size convolutional network; inputting a double-layer long-short-term memory network for sequence-level modeling, and outputting base reconstruction probability distribution; and constructing positive and negative sample pairs, calculating comparison loss, combining cross entropy loss to form a joint loss function, and outputting a high-precision DNA sequence reconstruction result. The method has high accuracy and robustness under the conditions of complex noise and multiple types of errors.

The invention provides an invasive species identification method and device based on deep learning and DNA storage and electronic equipment, and relates to the technical field of invasive organism prevention and control, and the method comprises the steps: obtaining a to-be-identified invasive species image, and generating a first DNA sequence of a to-be-identified invasive species in the invasive species image through a deoxyribonucleic acid DNA encoder; obtaining a plurality of second DNA sequences to be hybridized from the invasive species database, and obtaining the hybridization yield of the first DNA sequence and each second DNA sequence by using a hybridization yield predictor; and determining the species category corresponding to the DNA sequence with the highest hybridization yield as the species category of the invasive species to be identified. According to the method provided by the invention, the strong feature extraction capability of deep learning is combined with the advantages of ultrahigh density and ultra-long stability of DNA as a data storage medium, so that end-to-end mapping and recognition from a species image to an exclusive DNA sequence thereof are realized.

A DNA-based storage system implements a sub-code architecture for error correction capability (ECC) purposes. The sub-code architecture enables a long DNA strand to be divided into two or more short DNA strands. Each short DNA strand has its own unique parity information. Additionally, each short DNA strand is separately decodable from the other short DNA strands. The parity information associated with a particular short DNA strand is used to correct any errors that occur or are detected during the decoding process. However, if the decoding and error correction processes are not successful using the parity information associated with the particular short DNA strand, global parity information is used to decode the particular short DNA strand and correct the errors. Global parity information includes information from each short DNA strand and the parity information associated with each short DNA strand.

A DNA-based storage system stores DNA strands that are divided into N tiers. Due to the nature of the DNA storage channel, certain types of errors occur less frequently toward the front of a DNA strand and occur more frequently near the end of the DNA strand. As such, each tier stores data having a different level of importance when compared with other types of data stored in the different tiers. Because data stored near the front of the DNA strand has fewer errors than data stored near the end of the DNA strand, the data stored near the front of the DNA strand is decoded more quickly when compared with data near the end of the DNA strand.

The invention discloses a coding optimization-based DNA data storage method, a coding optimization-based DNA data reading method and a terminal, and the method comprises the following steps: S1, obtaining binary data of to-be-stored data, pre-coding the binary data according to an optimization target of DNA storage coding, the optimization target of the DNA storage coding comprising that the total module consumption quantity for information expression meets a preset condition; s2, after a DNA molecular chain set expressed in a module combination form is obtained through module mapping coding, a corresponding DNA molecular chain is obtained in an assembly or synthesis mode. According to the method, pre-coding and module mapping cascade coding are introduced, based on a pre-synthesized module library, physical storage is carried out on electronic data through DNA assembly, pre-coding mainly refers to reduction of the number of bit 1, meanwhile, module mapping coding is introduced, DNA data storage based on the assembly technology is achieved, and the method has the advantages of being simple in structure, convenient to operate and high in practicability. A specific module combination is selected from a preset DNA module library to react and connect to form the DNA molecular chain, and compared with a synthesis technology, the speed and the cost of the method can be optimized.

A DNA-based storage system includes an error correction system operable to: (a) identify a DNA codeword from a DNA sequencing operation; (b) calculate an initial syndrome weight; (c) determine that the initial syndrome weight is greater than a predetermined threshold; (d) perform an alignment alteration in the information segment by: (i) selecting a skew point within the information segment; (ii) performing an indel operation on the information segment at the skew point; (iii) calculating a modified syndrome weight; (iv) comparing the initial syndrome weight with the modified syndrome weight; and (v) incorporating the indel operation into the information segment when the comparing indicates an improvement in the modified syndrome weight; (e) decode the modified codeword; and (f) transmit the contents of the output file to a computing device, the output file representing user data stored within the DNA molecule.

The invention discloses a multi-channel extensible automatic sample loading system for DNA storage and calculation and a control method. The system comprises a gas path control device, a multi-channel sample introduction device, a liquid flow control device, a multi-liquid-path liquid collection device, a micro-fluidic chip and an upper computer, operation control over the whole system is provided through the upper computer, a user can adjust the sample injection sequence and the reaction time of each channel, the liquid flow and the gas flow of each channel are monitored and adjusted in real time in an experiment, and multi-channel and high-precision automatic sample injection is achieved. According to the invention, accurate injection and automatic control of samples are realized, the efficiency and precision of sample treatment are greatly improved, and high automation, high-precision sample injection and multi-channel low cross contamination control capability are realized; the expandability is high, and modular expansion to hundreds of channels or even hundreds of channels is supported; meanwhile, the method is compatible with various application scenes, and is suitable for the fields of high-throughput DNA calculation, DNA information storage, biomedical detection and the like.

The present invention discloses an information storage method based on DNA coding. The method comprises the following steps: converting digital information to be stored into a quaternary code, and converting the quaternary code into a DNA sequence consisting of adenine A, cytosine C, guanine G, and thymine T according to a preset mapping rule, and using the chemical modification state of the nucleotide pairs to represent an additional information dimension; inserting error detection and correction codes at every predetermined number of base positions in the DNA sequence, dividing the encoded DNA sequence into multiple fragments of 100-150 bp in length, and adding specific recognition sequences and index markers at both ends of each fragment; utilizing a reversibly thermoresponsive DNA nanostructure as a carrier, selectively binding the DNA fragments to the carrier, and realizing hierarchical storage and rapid retrieval of information through a temperature gradient control system; the present invention can significantly improve the information density and lifespan of DNA storage, and provides a new technical path for large-scale, long-term, and secure molecular information storage.

The invention provides a novel block storage system and method based on a DNA storage medium. The method comprises the steps that an operation interface for reading and writing is provided for a user; an efficient reading and writing operation interface is provided for a user through a remote updating technology; most of a block device translation table is placed in DNA, and translation is accelerated by using a solid state disk, so that better performance is provided; the invention further relates to a garbage collection mechanism for efficiently collecting the garbage data in the block equipment, and by means of the method that garbage collection metadata and data are stored together, and invalid garbage data are delayed to be read, the garbage data in the block equipment are efficiently released at low cost, and fragmentation of the data is relieved.

The invention relates to the technical field of DNA information storage, and discloses a method for prolonging data storage time and application, the method comprises the following steps: data is converted into a DNA sequence with a preset length, DNA is synthesized and stored, primary amino groups in basic groups of the DNA are independently modified by protective groups, the protective groups are selected from-COR, and the primary amino groups in the basic groups of the DNA are independently modified by the protective groups. R is selected from alkyl of C1-C6, substituted or unsubstituted naphthenic base of C3-C8 or substituted or unsubstituted phenyl. According to the method for prolonging the data storage time, the degradation rate of DNA can be remarkably inhibited, the stability of the DNA can be improved so as to realize long-time stable storage of the data, and the method is particularly suitable for forming a DNA storage scene with limited conditions, namely, the method is suitable for DNA synthesis in large companies with advanced technologies and equipment and also suitable for large companies with advanced technologies and equipment. The method is also suitable for DNA synthesis of small companies, and has application prospects and potential.

The present invention discloses a method for optimizing DNA storage coding based on the RBS algorithm. This method first converts binary data into a base sequence and divides the sequence into three files according to base frequencies. Secondly, three methods, namely data block merging, RH hybrid coding, and character merging, are respectively used to encode the three files. Finally, rotation coding is used to convert binary data into a base sequence and divide it into short sequences of 120 nt each. The codewords generated by the present invention have a higher information storage density and better coding quality in DNA storage, improving the efficiency, practicality, and stability of DNA storage.

The application discloses a DNA information storage method with a preview function, comprising the following steps: S1, generating a binary sequence of an original file to be stored and a corresponding binary sequence of a preview file; S2, converting the binary sequence of the original file and the corresponding binary sequence of the preview file into a DNA base sequence of the original file and a DNA base sequence of the corresponding preview file, so that the whole DNA base sequence meets a constraint of synthetic biology; S3, judging whether a first type of DNA information sequence construction method or a second type of DNA information sequence construction method is adopted; S4, executing the first type of DNA information sequence construction method; and S5, executing the second type of DNA information sequence construction method. Compared with the prior art, the application realizes the file preview function on a traditional computer in a DNA information storage system, and brings great convenience to a file retrieval process of DNA storage.

The application provides a DNA storage method and a data information storage entity capable of realizing random lossless reading of data, and the DNA storage method comprises the following steps: S1, preparation of a DNA double-stranded structure; S2, preparation of a data information storage entity; S3, random lossless reading of DNA data; and S4, recycling of the data information storage entity. According to the DNA storage method provided by the application, the random access function is realized by using the DNA double-stranded structure, and the long-term storage function is realized by using the outer wrapping hydrogel material, random reading in a file system with a large number of files is realized, and the original data is ensured not to be lost, so that the application has a wide application prospect in the field of DNA storage.

The invention discloses a DNA sequence assembly method and system based on a dynamic variable order unitg-level graph, and relates to the technical field of bioinformatics and DNA storage. According to the method, a pseudo genome and a source perception k-mer index are constructed, a Mid-Max and Min-Mid two-stage variable order expansion strategy is adopted, a k value is dynamically adjusted to enhance the graph structure connectivity, and the problems that under the condition of low coverage rate or high error rate, an existing de Bruijn graph method is prone to breakage and path fuzziness is prone to being generated are effectively solved. According to the method, a hidden path is accurately repaired through node connection and splitting operation, and redundancy k-mer is filtered in combination with index continuity and prefix similarity, so that the assembly integrity and accuracy are improved, and meanwhile, the robustness of DNA data reconstruction is remarkably enhanced; the method is suitable for various high-noise and low-coverage-rate scenes such as genome assembly and DNA storage and reconstruction, and particularly shows excellent performance in practical application with high requirements on data integrity and reliability.

The invention discloses a design method of a file system architecture oriented to DNA storage block equipment, and belongs to the technical field of DNA storage. The problem of providing more convenient, efficient and abundant DNA storage services for upper-layer users is solved. The method comprises the following steps: constructing a physical layer in a file system oriented to DNA storage block equipment, defining a primer block, and constructing a method for reading and writing DNA data input by DNA data input equipment oriented to the DNA storage block equipment on the basis of the primer block; constructing a file system layer in the file system oriented to the DNA storage block equipment, and establishing a method for converting the primer blocks into logic data blocks in the file system layer; and constructing the file system oriented to the DNA storage block device and a read-write delay optimization method of the DNA data input device, and completing the overall design of the file system oriented to the DNA storage block device. According to the invention, the data access efficiency of DNA storage is improved.

The invention provides a DNA storage medium-oriented scalable vector graphics (SVG) image coding method and system, and the method comprises the steps: reading an SVG file, analyzing the SVG image to obtain a document tree containing a plurality of nodes, and distributing structure information for representing the structure position of the nodes in the document tree for the nodes; coding the nodes to generate node fragments, wherein the node fragments comprise label codes generated according to labels of the nodes and attribute codes generated according to attributes of the nodes; aggregating the plurality of node fragments according to the label codes thereof to form at least one aggregation block, the aggregation block comprising header information and the plurality of node fragments, the header information being used for indexing the node fragments contained therein; the at least one aggregate block is converted into at least one DNA base sequence, and error correction information for error verification or repair is added to the at least one DNA base sequence. According to the method, the encoding length is reduced while the semantic integrity of the SVG is maintained, the error-resistant capability is improved, and the progressive decoding capability is provided.

The application discloses a kind of biomimetic mineralization materials with high stable protection DNA and preparation method thereof.DNA molecule is self-assembled with divalent metal ion, and DNA / metal nanoparticle is obtained; polyelectrolyte layer is wrapped on the surface of DNA / metal nanoparticle by layer-by-layer assembly technology, and DNA / metal@LBL nanoparticle is obtained; polydopamine layer is deposited on the surface of DNA / metal@LBL nanoparticle, and DNA / Fe@LBL@PDA particle is obtained, which is biomimetic mineralization material with high stable protection DNA.The biomimetic mineralization material has the advantages of simple construction, high density and long-term stability, and can effectively protect the stability and integrity of DNA molecule in harsh external storage environment (such as ROS, high temperature, high salt, alkaline, humid, biological solvent and nuclease environment).The present application can provide technical support for DNA high-density storage and long-term stability storage, and has wide application value in the fields of biological medicine, genetic engineering, disease treatment and DNA storage.

A DNA data storage method, a reading method and a terminal based on coding optimization, the method comprising: S1: obtaining binary data of data to be stored, pre-coding the binary data according to the optimization target of DNA storage coding, the optimization target of DNA storage coding including that the total number of modules consumed for information expression meets a preset condition; S2: obtaining a set of DNA molecular chains represented by a module combination through module mapping coding, and obtaining the corresponding DNA molecular chains through assembly or synthesis. The present invention introduces pre-coding and module mapping cascade coding, based on a pre-synthesized module library, and physically stores electronic data through DNA assembly. The pre-coding in the present invention mainly refers to reducing the number of "bit 1", and at the same time, by introducing module mapping coding, DNA data storage based on assembly technology is realized, and a specific module combination is selected from a preset DNA module library for reaction connection into a DNA molecular chain, and its speed and cost can be optimized compared to synthesis technology.

The application discloses a robust multi-sequence reconstruction method based on maximum posterior probability in DNA storage, and comprises the following steps: decoding each sequence in a cluster by using an improved BCJR decoder; converting each sequence in the cluster into corresponding time sequence representation; determining the weight of each sequence; and deducing a MAP algorithm formula of robust multi-sequence decoding, and integrating the sequence weight into joint posterior probability calculation to inhibit the influence of outlying sequences. By proposing a base IDS channel model, the BCJR decoding algorithm is improved, so that the defects that the existing statistical inference sequence reconstruction method is only suitable for binary error correction code are overcome. Therefore, the application can process the quaternary error correction of the base form in the DNA sequence.

The invention relates to a DNA data storage molecular tag based on nanopores and a preparation method and application thereof, and belongs to the technical field of DNA storage. The molecular tag is prepared by modifying azido polysaccharide onto an alkyne-containing DNA chain through a click chemical reaction. Hybridizing and fixing the molecular tag and a DNA bracket chain containing a specific notch structure, and scanning by using a glass nanopore; when the molecular tag passes through the nanopore, a characteristic ionic current blocking signal is generated, and accordingly data coding is achieved. The molecular tag disclosed by the invention is low in cost and simple and convenient to operate; polysaccharide with wide sources and efficient click chemistry are utilized, so that the preparation cost and complexity are remarkably reduced; the physicochemical properties of polysaccharide molecules are stable, the consistency of read signal amplitudes is ensured, the decoding accuracy is high, the label structure stability is good, and a guarantee is provided for long-term storage of data; based on a reversible hybridization storage structure, data updating can be realized without synthesizing a new DNA chain.

The application discloses a DNA storage coding method based on a graph convolution network and a self-attention mechanism, and belongs to the technical field of coding in DNA storage. Specifically, a DNA coding sequence meeting a combination constraint condition is predicted, first, existing DNA coding is screened and data is cleaned to construct a DNA storage coding training set; second, a prediction model based on a graph convolution neural network and a self-attention mechanism is trained, and the self-attention mechanism is used to capture the relationship of local DNA coding; then, the coding data processed into a graph is input into the prediction model to perform coding prediction meeting the combination constraint; finally, a DNA storage coding set meeting the condition is output. The application constructs a DNA storage coding training set, trains a graph convolution self-attention neural network, better captures the relationship between codings, and adopts a learning-based prediction model to perform DNA storage coding, so that the application has high coding efficiency when processing codings with complex constraints.

The invention belongs to the crossing field of DNA digital storage and bioinformatics, and discloses a DNA sequencing read clustering method and system based on characterization learning, and the method comprises the steps: carrying out the preprocessing of an original DNA sequencing read, and obtaining a sequencing read and a corresponding variant 1 and variant 2 set; carrying out characterization learning on the DNA sequencing read segments through a deep learning model based on the sequencing read segments and the corresponding variant 1 and variant 2 sets; and based on the DNA sequencing read after characterization learning, realizing clustering of the DNA sequencing read through a fine tuning model. According to the method, the problem of clustering difficulty caused by sequencing errors in DNA storage is solved.

The present application discloses a system and encoding / decoding method suitable for DNA storage of PB-level data. The data storage system includes multiple DNA clusters. The DNA cluster contains a data chain formed after binary data encoding, an XOR redundant chain generated by the data chain, an address chain of the DNA cluster at the storage system location, a basic information chain of the stored file, and a redundant chain generated by the XOR of the address chain and the file information chain. When a save operation is performed on a file with a preset suffix, a user-mode monitoring program receives an execution instruction and copies the file to a working directory, and encodes or decodes the file according to the file suffix. The result of the encoding or decoding operation is copied back to the original file directory. The present application enables the total capacity of the DNA database to reach above the PB level, allowing DNA storage to realize the application potential of high data density. At the same time, it can realize the automatic encoding of binary data and the automatic decoding of base sequences, streamline and automate the entire encoding and decoding process, and facilitate subsequent data management and archiving.

The invention discloses a DNA storage encryption and steganography method based on a non-natural basic group, and relates to the technical field of data storage. According to the method, a non-natural base pair (UBPs, NaM-TPT3) is introduced to a DNA sequence of coded information, during reading, the information sequence generates signal termination at the UBPs position, and a complete DNA sequence cannot be obtained, so that the purpose of encrypting DNA storage information is achieved, and DNA information can be smoothly read and decoded through bridge base isoTAT-mediated base conversion PCR (Polymerase Chain Reaction). Besides, a non-natural basic group is added to the 5'end of the index primer to prevent the index primer and a similar sequence from generating non-specific amplification, further, a natural primer is used for marking error information, a primer containing UBP is used for marking target information, and the target of information steganography is achieved through mixed storage. According to the method, encryption and steganography of DNA storage are realized by using a UBP technology, so that the security of DNA data storage is improved.