96results about "DNA computers" patented technology

The present disclosure, among other things, provides machine-learning technologies for identifying and localizing particular genomic elements (e.g., gene elements and / or regulatory elements) within nucleotide sequences, such as DNA and / or RNA sequences. In certain embodiments, similar to the manner in which image processing methods can be used to localize particular objects in images at pixel level resolution, referred to as “segmentation,” systems and methods of the present disclosure predict presence and locations of certain genomic elements within nucleotide sequences, thereby “segmenting” nucleotide sequences. Accordingly, genomic element segmentation technologies described herein may be used to generate annotations that identify and label portions of nucleotide sequences according to their predicted (e.g., via machine learning models described herein) function—e.g., as protein-coding genes, untranslated regions, splice sites, promotors, enhancers, etc. Among other things, these genomic annotations may be used to inform underlying biological processes driving diseases and facilitate development of new therapies.

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 cryoelectron microscope density map refinement method based on a mixed attention mechanism belongs to the field of bioinformatics, and comprises the following steps: firstly, constructing a training data set containing an experimental density map and a corresponding atomic structure, extracting feature embedding representation of the atomic structure by using a protein large language model, and generating a corresponding simulated density map according to the atomic structure; cutting each experimental density map and the corresponding simulated density map into blocks; thirdly, the experimental density map blocks and the structural features are embedded and input into a Transform deep learning network based on a mixed attention mechanism, and prediction density map blocks are generated; then calculating a loss difference value between each group of prediction density map blocks and the corresponding simulation density map block, and updating network parameters through a back propagation difference value; and finally, segmenting a to-be-processed cryoelectron microscope density map into a plurality of density map blocks, and predicting and assembling the density map blocks through the trained network to obtain a final refined density map. The method can improve the quality of the density map, and is high in robustness.

The invention provides a Word document processing method and system based on a DNA genetic model, and relates to the technical field of document processing, and the method comprises the following steps: carrying out homogenization determination on two basic Word documents; splitting the document which is judged to be homogeneous into a chain A and a chain B, and performing variation processing on a title block; crossing and recombining to form two sub-documents; and evaluating the sub-documents based on the adaptive function, and adding the sub-documents with evaluation results higher than a threshold value into a resource pool. According to the method, diversified documents are generated by simulating a DNA genetic mechanism, the document generation efficiency is improved, different user requirements are met, and the content creation cost is reduced.

A messenger RNA (mRNA) vaccine has emerged as a promising direction to combat the COVID-19 pandemic. This requires an mRNA sequence that is stable and highly productive in protein expression, features to benefit from greater mRNA secondary structure folding stability and optimal codon usage. Sequence design remains challenging due to the exponentially many synonymous mRNA sequences encoding the same protein. The present disclosure presents embodiments of a linear-time approximation (LinearDesign) reducing the design to an intersection between a Stochastic Context Free Grammar (SCFG) and a Deterministic Finite Automaton (DFA). Embodiments of the LinearDesign may implement an mRNA sequence design using much reduced time with very limited loss. Various methodologies, e.g., finding alternative sequences based on k-best parsing or directly incorporating codon optimality, are presented for incorporating the codon optimality into the design. Embodiments of the LinearDesign may provide efficient computational tools to speed up and improve mRNA vaccine development.

The invention provides a multimodal transport alternative path and transport scheme generation method based on road network node interruption. The method comprises the following steps: acquiring road network interruption information; if the road network interruption information is updated, for each original path, judging whether the original path comprises the road network interruption information or not; if yes, marking a break point in the original path, constructing an upstream candidate loading and unloading point set and a downstream candidate loading and unloading point set based on a first constraint condition, and selecting a loading and unloading node from each of the upstream candidate loading and unloading point set and the downstream candidate loading and unloading point set by adopting an upper-layer model by taking the minimum duration as a first objective function; inputting the selected first loading and unloading node and the selected second loading and unloading node into a lower-layer model, wherein the lower-layer model adopts a genetic algorithm to construct a multimodal transport replacement path set; and when the transportation unit travels to one end of the path, determining a final path based on the consumed time of each path, and constructing a multimodal transportation scheme.

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.

Methods, systems, and devices for encoding data for storage in genetic material are disclosed. For example, a computing system can segment user data into a plurality of data blocks and generate seed data characterizing a plurality of fountain code seeds. Additionally, the computing system can, for each data block, implement a set of operations to generate one or more data packets. In some instances, the set of operations can include, for each of the plurality of fountain code seeds, determining a bit value and a corresponding meta code value, and determining which of the fountain code seeds has a meta code value for the bit value that matches a value for the bit position identified in the metadata. Furthermore, the computing system can, for each data packet, cause implementation of a second set of operations to synthesize a polynucleotide strand from at least the bit values of the corresponding data packet.

Compositions, methods, and systems for handling liquids, for example, liquids containing one or more biological substances or chemical reagents, or combinations thereof. The liquid can be an "ink" containing nucleic acids (e.g., DNA) for "nucleic acid "printing" or "writing." These nucleic acids can include one or more components of nucleic acid molecules that encode digital information ("identifiers") that can be used in methods and systems for encoding digital information in nucleic acid. Described in this specification are technologies including an ink supply system and associated ecosystem for a DNA writing device for use with the technologies for encoding, storing, reading, and / or processing digital information in nucleic acid molecules.

Synthetic molecular tags are placed on an item at various points in a supply chain to create a molecular record of movement through the supply chain. Associations between each unique synthetic molecular tag and individual locations in the supply chain are stored in an electronic record which may be maintained in the cloud. The synthetic molecular tags are collected from the item and sequenced to determine movement of the item through the supply chain by reference to the electronic record. The synthetic molecular tags can be used for identifying recalled items based on locations in the supply chain associated with a recall. The synthetic molecular tags may be polynucleotides such as deoxyribose nucleic acid (DNA). The item may be any type of item including food.

In a method for determining an optimal chemical modification for a base sequence of an RNA therapeutic agent, a base sequence modification module acquires, as learning data, biological properties when a plurality of chemical modifications are applied to a plurality of base sequences. Among the learning data, at least two sequences to which different chemical modifications are applied to the same base sequence are randomly selected and sequentially input into an artificial neural network, and the output values output for each of the at least two input sequences are compared. The process of training the artificial neural network is repeatedly performed so that the artificial neural network outputs a larger value as the biological properties of the input sequence are better, to generate an optimal chemical modification prediction model. Using the optimal chemical modification prediction model, an optimal chemical modification having excellent biological properties when applied to the base sequence of the RNA therapeutic agent is determined among the first to w-th chemical modifications.

Disclosed herein is an RNA editing tool for use in a system designed to measure RNA and manipulate specific cell types in vivo.The RNA sensor system comprises: a) a single-stranded RNA (ssRNA) sensor that comprises a stop codon and a payload, and optionally further comprises a normalization gene; and b) an adenosine deaminase that acts on RNA (ADAR), where the sensor can bind to target ssRNA to form a double-stranded RNA (dsRNA) that is a substrate for ADAR deaminase; the substrate comprises a mismatch within the stop codon; the mismatch can be edited by ADAR deaminase, and the edit can effectively remove the stop codon, allowing the payload to be translated and expressed.Also disclosed is a method for quantifying ribonucleic acid (RNA) levels using the RNA sensor system.

This invention involves the self-assembly of DNA molecules with divalent metal ions to obtain DNA / metal nanoparticles; coating the surface of the DNA / metal nanoparticles with a polyelectrolyte layer to obtain DNA / metal@LBL nanoparticles; and growing SiO2 on the surface of the DNA / metal@LBL nanoparticles to obtain stable DNA / Fe@LBL@SiO2 particles. A set of DNA double-stranded molecules with complementary base fragments is used. One base fragment is immobilized on the surface of the DNA / Fe@LBL@SiO2 nanoparticles to form addressable DNA / Fe@LBL@SiO2-ssDNA nanoparticles. The other complementary base fragment is immobilized on the surface of magnetic beads to form trapping magnetic beads. The trapping magnetic beads and the addressing DNA nanoparticles are selected by specific base pairing of base fragment primers, and the downstream hybridization products can be separated magnetically, ultimately achieving the separation objective.

In a method for determining an optimal chemical modification for a nucleotide sequence of an RNA therapeutic, a sequence modification module acquires, as learning data, biological characteristics corresponding to when multiple chemical modifications are applied to multiple nucleotide sequences, creates an optimal chemical modification prediction model by repeatedly performing a process of randomly selecting, among the learning data, at least two sequences in which different chemical modifications are applied to the same nucleotide sequence, sequentially inputting the selected sequences into an artificial neural network, and training the artificial neural network to compare output values for the input sequences and output a higher value as the biological characteristics for the input sequence are better, and uses the model to determine, as an optimal chemical modification, a chemical modification showing the best biological characteristics when applied to the nucleotide sequence of the RNA therapeutic, among first to wth chemical modifications.

The application belongs to the technical field of biological computing, and discloses a ternary addition system and a computing method based on DNA strand displacement, which comprises an input unit, a computing unit and an output unit. The input unit adds the input information to the corresponding computing module. The computing unit comprises nine modules, each of which is provided with a competitive blocking circuit and a carry computing gate, and dynamically selects a result bit 1 or 2 and generates a carry signal. The output unit outputs the digital information of 0-2 according to the fluorescent signal of the result bit, extracts the next bit carry information generated by the carry computation, amplifies the signal and then adds it to the next bit computation. The application breaks through the limitation of the number of DNA computing bits through the cooperation of the ternary gate control architecture and the fuel chain amplification, can accurately calculate the ternary addition, can expand the number of bits calculated, can realize 10-bit addition operation, and can be integrated with the expansion of the multiplication logic, thereby providing a universal framework for the molecular arithmetic unit.

The present invention is directed to a single input multiplex decision expression system, and a method of using same, such as for expressing a reporter protein.

Provided are a method and system for storing information using DNA. The method comprises: 1) obtaining a DNA fragment attribute library, wherein the DNA fragment attribute library comprises a plurality of DNA molecules, and comprises a retrieval table of storage object attributes and the DNA molecules, and each DNA molecule comprises double-stranded DNA, which represents the storage object attribute, and a single-stranded sticky end for connection; 2) on the basis of the retrieval table, encoding information to be stored, so that same is directly mapped to a corresponding DNA molecule in the DNA fragment attribute library; 3) acquiring corresponding DNA fragments from the DNA fragment attribute library, and connecting same, so as to obtain a connected DNA molecule; and 4) storing the connected DNA molecule. The method and system can be extended to different data types and different application scenarios, and prevent an oligonucleotide sequence from being repeatedly synthesized during storage, thereby greatly reducing storage cost.

The present disclosure provides a method, a device, and a system for storing information in a molecule. The method includes: obtaining information to be stored, wherein the information to be stored has one or more bit-groups, a position of each bit-group in the information to be stored is represented by a first address, a value of each bit-group is represented by a first content, and each bit-group has one or more bits; determining a molecule module corresponding to at least one bit-group of the one or more bit-groups, wherein the molecule module includes a first molecule module, and the first molecular module is configured to represent both the first address and the first content of a corresponding bit-group; and generating a composition based on the determined molecular module such that the composition corresponds to the information to be stored.

Described herein are systems and methods for quality control of polynucleotides. The provided systems and methods for quality control are performed before, during, or after synthesis or storage of the polynucleotides. Further provided herein are system and methods for performing quality control of a surface, for example for synthesis or storage of polynucleotides.

Systems and methods for polynucleotide quality control are described herein. The provided systems and methods for quality control are performed before, during, or after the synthesis or storage of polynucleotides. Also provided herein are systems and methods for quality control of surfaces, such as surfaces for synthesis or storage of polynucleotides.

The application discloses a kind of based on reinforcement learning's machine group cooperation data acquisition method, comprising the following steps: S1, constructs environment mathematical model, constructs the mathematical model of cooperation data acquisition in mobile crowd sensing scene and can be solved and can be analyzed, environment mathematical model includes: scene parameter construction, data value classification and cooperation data acquisition;S2, establish perception model, perception model is used in unmanned aerial vehicle mobile crowd data acquisition process cooperation perception target position, relative velocity and target quantity information, and perception model includes: distance perception and relative velocity perception.The based on reinforcement learning's machine group cooperation data acquisition method disclosed in the application combines multi-agent reinforcement learning and deep learning, utilizes deep neural network to solve the representation problem in wide state action space, and provides intelligent decision-making ability by the trial-and-error mechanism of reinforcement learning, enhances the ability of efficient collection of heterogeneous data in a generalized manner in multiple dimensions.

The invention discloses a method and a device for DNA storage coding and decoding and rules thereof. The method comprises the following steps: performing single-molecule sequencing on a reference sequence to obtain actual sequencing data of single-molecule sequencing; comparing the actual sequencing data with reference data of the reference sequence, counting the frequency of sequencing errors of each sequence fragment with the length of k in the actual sequencing data, and calculating the proportion of the sequencing errors of each sequence fragment with the length of k in the actual sequencing data, namely the error rate; and taking the sequence fragments of which the error rates exceed a threshold value as limiting conditions to be eliminated. According to the method provided by the invention, the DNA storage coding and decoding steps are simplified, and the complexity of data processing is reduced through the time sequence of the threshold elimination step.

A data storage system and method are provided, as well as systems and methods for fabrication, and writing and reading of data therein. The data storage system includes at least one population of molecular sequences including chains of basic molecular building -blocks, and defining at least one respective data-block encoding data in the data storage system. The data of the data-block is encoded in a sequence S = (π 1, π 2,..., π k..., π κ-1, π κ) of encoded letters {π k} associated with an alphabet ∑ ≡ { σm } |m= 1 to M, which are encoded according to the types of basic molecular building -blocks appearing at k respective location along storage segments of the molecular sequences of the population. The molecular sequences include a number Z of different types of basic molecular building -blocks {En}|n=1 to z, while the alphabet ∑ has a size M strictly greater than the number Z of types of building -blocks. Each alphabet letter om is associated with a vector {Pmn}|n=1 to z indicative of occurrences of basic molecular building-block En of type n in the alphabet letter σm. Accordingly each encoded letter π κ at location k in the storage segments of molecular sequences of the data-block / population, is mapped to a corresponding alphabet letter om by determining a match between the occurrence of basic molecular building-blocks of different types at that locations k of the molecular sequences of the population, with the vector {Pm n}|n=1 toz associated with the alphabet letter σm. In some implementations the component Pm n of the vector { Pn}m|n=1 to z associated with alphabet letter σm is indicative of a probability that a basic molecular building-block En of type n, 1 ≤ n ≤ Z, appears at the location k of the storage segment of a molecular strand of the at least one population in case the letter π κ encoded at that location k corresponds to the alphabet letter σm.

Using nucleotide architectures to very closely and precisely place chromophores on a nucleic acid template to form dye aggregates that produce quantum coherent excitons, biexcitons, and triexcitons upon excitement to create excitonic quantum wires, switching, and gates that would then form the basis of quantum computation. Creating the various excitons and controlling the timing of the excitons would be performed using light of the corresponding wavelength and polarization to stimulate the corresponding chromophores.

Disclosed are a method and apparatus for DNA storage encoding / decoding and rules thereof. The method comprises: executing single-molecule sequencing on a reference sequence, and acquiring actual sequencing data of the single-molecule sequencing; comparing the actual sequencing data with reference data of the reference sequence, counting the frequency, in the actual sequencing data, of sequencing errors of each sequence segment having a length of k, and calculating the proportion, in the actual sequencing data, of sequencing errors of each sequence segment having a length of k, that is, the error rate; and performing removal by using a sequence segment, the error rate of which exceeds a threshold, as a limiting condition. In the method of the present invention, the steps of DNA storage encoding / decoding are simplified, the time sequence of the steps is eliminated by using a threshold, and the complexity of data processing is reduced.

The embodiment of the invention provides an encoding method, a decoding method and related equipment applied to DNA storage. The encoding method comprises the following steps: acquiring a to-be-encoded first base sequence and a first mapping relation; the first mapping relation is a mapping relation between the base fragments with various lengths and the coded values; matching the first base sequence with a base fragment contained in the first mapping relation to obtain a matching result; dividing the first base sequence into a plurality of segments to be coded according to a matching result; according to a first mapping relationship, converting each fragment to be coded in the first base sequence into a coded value to obtain a numerical sequence; and converting the numerical sequence into a second base sequence. According to the encoding method and the decoding method provided by the embodiment of the invention, DNA storage is carried out, and higher confidentiality and safety are achieved.

The invention relates to the technical field of molecular computing and information security crossing, in particular to an information security protection method and system for programmable access control of a molecular system. According to the method, a general signal is input into a molecular system to trigger a pre-closed state, a real information access interface is hidden, a unified molecular decoy response signal is output, and active defense is achieved; after an access request containing an access signal and a rollback factor is received, rollback factor legality and permission matching degree verification is completed in sequence; the closed state is maintained during unauthorized access, and the hierarchical backtracking reaction is triggered through rollback factor combination during authorized access, and the hierarchical information fragments corresponding to the authority are gradually released. According to the method, the crossing from passive authentication to active hiding, from static permission to dynamic grading and from extensive recovery to precise maintenance is realized, and the safety, controllability and robustness of the molecular information system in a complex environment are remarkably improved.

The present disclosure discloses a spatially layered DNA storage method for large-scale oligonucleotide pools, employing a DNA spatially layered coding method to enable real-time data readout; the unordered DNA strands are spatially organized into an addressable base array, and the live data are encoded chronologically into sequential coding layers, wherein bases are mapped to crosscutting identical positions across all strands; for recovery, a live and accelerated approach to spatially form a coding layer is provided, and the error correction codes are utilized to fill the base gap, enabling continuous, real-time streaming; a layer-wise spatial-temporal recovery method is presented to facilitate an error-free data stream, spatially achieving instant consensus of multiple signals within a layer, and temporally updating flow signals via the previous successfully decoded layers; the error correction and readout methods provided by the present disclosure can match the sequencing process, achieving simultaneous sequencing and real-time decoding.

The present disclosure relates to methods and compositions for producing a DNA sequencing library for one or more DNA sequences of interest using a k-mer analysis strategy. The present disclosure further provides methods of producing a DNA library for analysis of one or more DNA sequences of interest and methods of identifying a DNA sequence variation or a modification in a DNA sequence of interest. Aspects of the present disclosure further relate to a DNA library produced by the methods of the present disclosure.