31 results about "Genomic information" patented technology

The invention relates to the technical field of intelligent agriculture and crop models, and particularly discloses a corn whole growth period simulation model construction method based on gene information. The method comprises the following steps: firstly, obtaining whole genome re-sequencing data of a target corn population and multi-growth-stage phenotype data of continuous years at the same ecological point, and dividing the population into a plurality of subgroups with consistent genetic backgrounds based on the re-sequencing data; and then, by adopting a strategy of'single family parameter inversion-subgroup template construction-secondary optimization and calibration on a single genotype under the constraint of the subgroup template ', the genetic subgroup characteristics based on the genome are associated with an APSIM crop model, and a high-precision corn growth period prediction model is constructed. According to the method, the defects that a traditional crop model is low in large-scale breeding material parameter calibration efficiency and prone to falling into local optimum are overcome, and the method is particularly suitable for efficient and accurate growth period prediction and adaptability evaluation on a large number of breeding materials in a unified ecological region.

The invention discloses a ganoderma lucidum binuclear genome assembly method based on haplotype analysis, and belongs to the technical field of bioinformatics. The purpose of the present invention is to overcome the accuracy and accuracy of high hybrid genome assembly. The invention provides a ganoderma lucidum binuclear genome assembly method based on haplotype analysis, which comprises the following steps: obtaining mononuclear ganoderma lucidum cells, respectively carrying out whole genome sequencing by utilizing Illumina NovaSeq, Nanopore, Hi-C and PacBio HiFi, and obtaining accurate genome information according to the sequencing data of the Illumina NovaSeq and the sequencing data of the Nanopore. And an assembly strategy of haplotype separation is realized.

The invention discloses an aegilops variabilis whole genome SNP site combination, a probe, a chip and application of the aegilops variabilis whole genome SNP site combination, the probe and the chip. The aegilops variabilis whole genome SNP site combination is composed of 10K SNP sites composed of 4K Dv subgenome SNP sites and 6K Nv subgenome SNP sites. According to the method, the genome information of the aegilops tauschii can be detected in a high-quality, high-efficiency and high-throughput manner, so that an efficient detection technical means is provided for molecular breeding application of the excellent genes of the aegilops tauschii and the chromosome segments of the excellent genes, and an efficient detection tool is provided for exploration and breeding utilization of the excellent genes.

Disclosed herein are methods for single-cell sequencing. In some examples, the methods include enriching a sample comprising a plurality of cells for cells of interest to produce an enriched cell sample; isolating one or more cells of interest in the enriched cell sample; and obtaining sequence information of one or more polynucleotides from each of the one or more isolated cells. Obtaining sequence information may include generating a molecularly indexed polynucleotide library from the one or more isolated cells. Enriching the sample may include focusing cells of interest in the sample using acoustic focusing.

This invention discloses a method for constructing and analyzing a genome-scale metabolic network model of *Paragonimus denitrifyingus*, belonging to the field of systems biology. The method includes: whole-genome annotation; obtaining global metabolic response data of *Paragonimus denitrifyingus*; automatically retrieving genomic information and constructing Model 1 based on the species code and genome annotation results of *Paragonimus denitrifyingus* in the KEGG database; constructing Model 2 by identifying homologous proteins in the *Paragonimus denitrifyingus* genome through homology searching of proteins in the target organism based on a pre-trained Hidden Markov Model; and integrating Model 1 and Model 2. This invention allows for the efficient design and modification of denitrification engineering, achieving precise control of nitrogen degradation processes. Compared to existing metabolic engineering methods, this invention effectively reduces the workload of exploratory experiments and greatly advances a deeper understanding of the nitrogen degradation characteristics of *Paragonimus denitrifyingus*.

This invention relates to the field of smart agriculture and crop modeling technology, specifically disclosing a method for constructing a maize full-growth-period simulation model based on genetic information. The method first acquires whole-genome resequencing data and multi-growth-stage phenotypic data of a target maize population over several consecutive years at the same ecological location. Based on the resequencing data, the population is divided into several subpopulations with consistent genetic backgrounds. Subsequently, using a strategy of "single-family parameter inversion – subpopulation template construction – secondary optimization and calibration of single genotypes under subpopulation template constraints," the genetic subpopulation characteristics based on the genome are correlated with the APSIM crop model to construct a high-precision maize growth period prediction model. This invention overcomes the shortcomings of traditional crop models, such as low efficiency in parameter calibration for large-scale breeding materials and susceptibility to local optima. It is particularly suitable for efficient and accurate growth period prediction and adaptability evaluation of a large number of breeding materials within a unified ecological zone.

The invention discloses a corn genetic typing primer combination suitable for a nanopore sequencing platform and application, the primer combination comprises at least one of 11 pairs of ONT primers, and the sequences of the primers are shown as SEQ ID NO: 1-SEQ ID NO: 22. The primer can specifically amplify a target area with rich heritable variation in a corn genome, PCR products obtained through amplification are mixed and then subjected to nanopore on-machine sequencing, the target rate of the amplification products is counted by analyzing species attributes and genome comparison positions of sequencing sequences and combining experimental data of a to-be-detected sample, known genome information is associated, and the target area of the to-be-detected sample can be identified according to the target rate of the to-be-detected sample and the target area of the to-be-detected sample. And the purity and identification accuracy of the corn seeds are judged. The primer combination has maize material specificity and intra-population compatibility, can economically and efficiently complete genotype identification of maize inbred lines and hybrid population offspring, and can be applied to maize variety authenticity verification and breeding material genetic background analysis and screening.

This invention discloses a method and system for selecting functional gene variant sites, relating to the field of gene site selection. The method includes: acquiring chromatin accessibility distribution information across the entire genome; performing convolutional block transformation based on the accessibility distribution information to obtain accessibility feature values; determining genomic information across the entire genome based on regulatory maps; determining an initial weight value set based on the accessibility feature values ​​and genomic information; the initial weight value set is a set of initial weight values ​​corresponding to each of the accessibility feature values ​​and genomic information; inputting the accessibility feature values, genomic information, and the initial weight value set into a site selection model, and outputting selected functional gene variant site information and regulated susceptibility gene information; the selected functional gene variant site information includes: site variant bases that meet set threshold conditions and their corresponding site coordinates; this invention can improve the selection efficiency of functional gene variant sites.

This invention discloses a primer combination for maize genotyping suitable for nanopore sequencing platforms and its application. The primer combination includes at least one of 11 pairs of ONT primers, the sequences of which are shown in SEQ ID NO: 1-SEQ ID NO: 22. The primers of this invention can specifically amplify target regions rich in genetic variation in the maize genome. The amplified PCR products are mixed and then sequenced using nanopore sequencing. By analyzing the species attributes and genome alignment positions of the sequencing sequences, combining experimental data from the test samples to calculate the targeting rate of the amplified products, and associating them with known genomic information, the purity and identification accuracy of maize seeds can be determined. This primer combination combines maize material specificity with population compatibility, enabling economical and efficient genotyping of maize inbred lines and hybrid populations. It can also be applied to verify the authenticity of maize varieties, analyze the genetic background of breeding materials, and screen for genotyping.

The application discloses a high-quality pig creating and breeding method, which comprises the following steps: 1) a certain blood structure of purebred Luchuan pigs is screened through molecular pedigree construction based on genome information, and the screened Luchuan pigs are used as female parents to cross with Duroc boars to generate Duroc-Luchuan crossbred pigs; 2) the Duroc-Luchuan crossbred pigs are used as female parents to cross with Barcshires boars to generate Bar-Duroc-Luchuan crossbred pigs; 3) the Bar-Duroc-Luchuan crossbred pigs are used as female parents to cross with Duroc boars to generate Duroc-Bar-Duroc-Luchuan crossbred pigs; 4) based on the Duroc-Bar-Duroc-Luchuan crossbred pigs, male and female pigs meeting the breeding target are selected according to a selection index to realize horizontal cross fixation, and an excellent horizontal cross offspring is selected to form a breeding core group; and 5) the core group in the step 4) is used as a zero generation group, a group succession breeding method is adopted, whole genome selection and genome prediction and the like are used to estimate a genome breeding value of breeding pigs and predict a phenotype, and precise intelligent breeding selection and matching are realized.

In a data processing system 1 comprising a data providing device 10, a data processing device 20, and a data utilization device 30. The data providing device 1 comprises a transmission / reception unit 13 that transmits a plurality of pieces of metadata related to a plurality of pieces of genome information extracted from a plurality of pieces of genome data to the data processing device. The data processing device 20 comprises a metadata management unit 22 that manages the plurality of pieces of metadata, and a genome information processing unit 24 that acquires encrypted genome information corresponding to metadata retrieved from the plurality of pieces of metadata by the data utilization device, and processes the acquired genome information in an isolated execution environment by means of an encrypted processing logic of the data utilization device. The data utilization device 30 comprises a search unit 31 that searches for metadata from the plurality of pieces of metadata, and a transmission / reception unit 32 that transmits the encrypted processing logic for the retrieved metadata to the data processing device and receives a processing result from the data processing device.

The application discloses a Ganoderma lucidum double-nucleus genome assembly method based on haplotype analysis and belongs to the technical field of bioinformatics. The application aims to overcome the precision and accuracy of high-hybrid genome assembly. The application provides a Ganoderma lucidum double-nucleus genome assembly method based on haplotype analysis, obtains single-nucleus Ganoderma lucidum cells, respectively performs whole genome sequencing on the cells by using Illumina NovaSeq, Nanopore, Hi-C and PacBio HiFi, obtains precise genome information from Illumina NovaSeq sequencing data and Nanopore sequencing data, and realizes a haplotype separation assembly strategy.

The invention relates to the technical field of genome information analysis, in particular to a local pig optimal heterosis prediction method based on genome information. According to the method, pure parents with clear genetic backgrounds are accurately identified and screened out by utilizing high-density SNP marker information covering a whole genome, a reference population is constructed, large-scale hybridization propagation is simulated, structured virtual population data is formed, and multi-character phenotype data of filial generations are standardized and weighted, so that the genetic backgrounds of the filial generations are optimized, and the genetic backgrounds of the filial generations are optimized. The method comprises the following steps of: dividing a plurality of characteristic groups such as a production performance type and a reproductive performance type, and analyzing the correlation between phenotypic deviation and genotype in each group, so as to separate and quantify dominant effect caused by heterozygous genotype and recessive effect caused by homozygous genotype, construct explicit and recessive weight parameters, and determine the genetic relationship between the dominant effect and the recessive effect; finally, the non-additive effect parameters are superposed to a traditional additive breeding value model, direct quantitative prediction of heterosis is achieved, and therefore the accuracy and efficiency of hybrid combination matching are greatly improved.

This invention discloses a wheat ultra-high-density gene chip probe and its preparation method, belonging to the fields of plant functional genomics, population genetics, and molecular breeding technology. Based on wheat pan-genome information, this invention uses resequencing data and exon capture sequencing data from large-scale natural wheat populations to perform variation analysis and obtain ultra-large-scale whole-genome variation information. High-quality SNPs and INDEL loci with population and individual representativeness are obtained through filtering and screening. Simultaneously, harmful mutation sites are identified, and publicly published genetic loci related to important wheat yield and quality traits are integrated and extracted. Polymorphic loci regions are determined by combining genome annotation and variation annotation. Finally, ultra-high-density liquid-phase probes are synthesized at the pan-genome level. Because this invention only sequences target gene regions, it reduces sequencing costs by more than 90% for the same gene sequencing depth.

The invention discloses a liquid-phase probe targeted capturing and library building method for adenovirus. The method comprises the following steps: S1, probe design: S1, designing a plurality of biotin-labeled adenovirus probes; s2, sample treatment and DNA purification; s3, carrying out fragmentation treatment on the double-chain cDNA, and carrying out terminal repair and linker connection, PCR amplification and magnetic bead purification to obtain an initial library; s4, mixing the initial library with an adenovirus probe, a blocker and a blocking mixed solution, hybridizing, purifying by magnetic beads, adding a fast hybrid mixed solution and a fast hybrid enzyme to promote hybridization, finally adding streptavidin binding beads and a fast capture buffer solution, and eluting to obtain an adenovirus enriched library; and S5, amplifying the enriched library by using a high-fidelity enzyme, and adding magnetic beads for purification. According to the present invention, with the liquid phase probe targeting capture technology, the core pain points such as low-load missing detection, incomplete serotype coverage, genome information loss, poor high-throughput adaptability and the like in the adenovirus detection are effectively solved, and the core technical support is provided for the adenovirus molecular diagnosis and the public health prevention and control.

The invention discloses a campylobacter jejuni liquid-phase probe targeted capturing and library building method and a kit thereof, and belongs to the technical field of germ detection. Specific probe enrichment, magnetic bead purification and high-throughput sequencing are combined, and the problems that in the prior art, low-load detection is difficult, information is incomplete, and operation is tedious are solved. Aiming at the characteristics of wide food-borne transmission, multiple low-load samples and strong complex matrix interference of campylobacter jejuni, low-load accurate detection, whole-genome information analysis and high-throughput standardized operation are realized through a liquid-phase probe targeted capture technology; the method is suitable for large-scale sample detection in the fields of food safety detection, clinical diagnosis, public health research and the like.

The application discloses a multi-gene discovery network construction method and device, equipment and a storage medium. The method comprises the following steps: acquiring genome information input by a user, constructing a discovery network among all to-be-encoded genes according to the genome information, and determining storage information of each to-be-encoded gene; generating a DNA sequence according to the discovery network and the storage information, sequencing the DNA sequence, and obtaining a sequencing result; decoding the sequencing result, obtaining gene position information, judging whether there is an encoded gene according to the gene position information, quickly and efficiently finding the corresponding gene during decoding, saving the gene searching time, quickly detecting the gene report error, avoiding the sequencing result error caused by multiple variations and the sequencing itself, and improving the speed and efficiency of the multi-gene discovery network construction.

An integrated data repository may be generated that includes genomics information and health insurance claims data information for a common group of individuals. A data processing pipeline may be implemented with respect to information stored by the integrated data repository. The data processing pipeline may include a number of sets of data processing instructions that are executable to analyze specified information stored by the integrated data repository and generate different datasets. The datasets may be analyzed to determine an impact of characteristics of individuals and / or an amount of impact of treatments provided to individuals in which a biological condition is present.

The invention provides a local livestock and poultry traceability method based on an SNP marker, and relates to the field of variety traceability, and the method comprises the steps of traceability gene bank construction, genetic relationship determination, traceability identification based on genome data, and traceability identification process and result determination. Wherein the traceability gene pool construction comprises source gene pool sample collection, sample collection and information recording, gene analysis and data generation, and traceability gene pool establishment; the genetic relationship judgment comprises repeated individual identification and paternity test; the traceability identification based on the genome data comprises repeated individual identification based on genome information and parent-child relationship identification based on the genome information; the traceability identification process and result judgment comprises sample receiving and quality control, data comparison and analysis and hierarchical result judgment. According to the method, SNP marker information is obtained through a genomics technology, accurate source tracing of livestock and poultry meat products is achieved through genetic relationship analysis, and the counterfeit and shoddy phenomena are effectively eradicated.

Disclosed herein are methods for single-cell sequencing. In some examples, the methods include enriching a sample comprising a plurality of cells for cells of interest to produce an enriched cell sample; isolating one or more cells of interest in the enriched cell sample; and obtaining sequence information of one or more polynucleotides from each of the one or more isolated cells. Obtaining sequence information may include generating a molecularly indexed polynucleotide library from the one or more isolated cells. Enriching the sample may include focusing cells of interest in the sample using acoustic focusing.

The invention provides a polyploidy genome apparent data resolution analysis method which comprises the following steps: S1, acquiring original data, removing linkers and filtering low-quality sequences; s2, carrying out single-ended comparison on the reference genome by using bowtie2 software and taking-k'n 'as a parameter, and screening comparison results; s3, recording double-end matched Reads and matched chromosome numbers; s4, dividing the reference genome into a plurality of sets, and independently constructing a reference genome index for each set of genome; s5, extracting sequences according to the records obtained in the step S3, and distributing the sequences to corresponding subgenomes according to chromosome numbers; and S6, comparing each group of sequences with corresponding sub-genomes according to a double-end comparison process, and finally identifying peaks information of each group of genomes, thereby completing the polyploidy genome apparent data resolution analysis. According to the method, by optimizing comparison parameters and adding a subsequent sequence identification screening strategy, apparent data between homologous chromosomes are accurately distinguished, and accurate distinguishing of genetic structures is achieved.

The invention discloses a method for detecting chromatin modification and whole genome information based on single molecule sequencing and application of the method. The invention provides a single molecule long read sequencing platform and a sequencing technology capable of researching protein-DNA interaction under single cell resolution, and the method can accurately analyze epigenetic information such as chromatin modification and the like in a single cell. Comprising histone covalent modification and a binding distribution mode of chromatin binding protein in a genome. According to the construction method of the long-read sequencing library and the single-molecule long-read sequencing data obtained by single-molecule sequencing based on the library, the data can be applied to analysis of repetitive sequences of each copy in a genome and chromatin modification of a'blacklist 'region by analyzing the data.

The application discloses a gastric cancer progression risk assessment system, and belongs to the technical field of bioinformatics and medical diagnosis. The system comprises a genomic data acquisition module, a core genomic variation feature construction module, a population structure correction module, a risk site identification module, a multi-site risk scoring module, a disease progression prediction module, and a risk judgment and report module. By deeply mining the core genomic information of the strain, filtering the recombination region and correcting the population structure, the strain risk sites significantly related to the progression of host gastric mucosa lesions are accurately screened, and then a risk scoring model is constructed, so that the precise quantification of the gastric cancer progression risk based on the Helicobacter pylori strain genomic data is realized. The application provides a new auxiliary diagnosis and precise intervention tool for the clinic, and the evaluation and prediction accuracy and stability are high.

The invention belongs to the technical field of microorganisms, and particularly relates to sphingobium sp., a microbial preparation of the sphingobium sp. And application of the sphingobium sp. The new sphingolipid strain D-491 is separated and screened from the desert environment, has the functions of nitrogen fixation, IAA secretion, alkali stress resistance and the like, enriches microbial strain resources and genome information, and broadens the application scene of the sphingolipid strain.

DEPCT6618 / 04 / 2566 To provide a program or similar entity that extracts mutations that are important to... Automated genome-based therapy. The program then allows the computer to process the search for training data, which Within it is genomic information obtained by reading the base sequences included in the submission and mutations. Genetic information based on submitted samples is recorded and linked for all genetic tests. This has been done many times in the past and has given rise to learning models (53) for output. Estimates related to genetic mutations are based on submitted genome data. This is obtained by reading the base sequence included in the submitted sample and inputting it through genome data assignment. Let's use genetic mutations as input and define them as output;

The present application belongs to the field of animal genetic breeding technology, and provides a high-efficiency embryo production donor cow screening method, which is characterized in that the method is to collect the phenotype data, pedigree and genomic information of the embryo production donor cow, establish a donor reference population, construct a kinship matrix based on the pedigree information and genomic information of the reference population, estimate the trait variance component according to a linear model; combine the kinship matrix of the reference population, the embryo production capacity trait variance component and the phenotype information to estimate the effect value of each SNP site of the reference population, select a linear model according to the genomic information and the SNP site effect value to construct a breeding model; input the genomic information and pedigree information of the individual to be tested, predict the gEBV of the individual based on the breeding model, and screen the high-efficiency embryo production donor cow according to the gEBV ranking. The present application establishes a genomic prediction technology of the high-efficiency embryo production donor cow, and can early and accurately screen the high-efficiency embryo production donor cow through the genomic information.

The application provides a local livestock and poultry traceability method based on SNP markers, relates to the field of breed traceability, and comprises traceability gene library construction, kinship determination, traceability identification based on genomic data, and traceability identification process and result determination; wherein, the traceability gene library construction comprises source gene library sample collection, sample collection and information recording, gene analysis and data generation, and traceability gene library establishment; the kinship determination comprises repeated individual identification and parent-offspring identification; the traceability identification based on genomic data comprises repeated individual identification based on genomic information and parent-offspring relationship identification based on genomic information; the traceability identification process and result determination comprises sample receiving and quality control, data alignment analysis, and hierarchical result determination. The method realizes accurate traceability of livestock and poultry meat products by obtaining SNP marker information through genomics technology and realizing accurate traceability of livestock and poultry meat products by using kinship analysis, and effectively prevents false and inferior phenomena.

The application provides an agarase AgaCA233, a mutant thereof and application. The application mines a beta-agarase of a GH16 family, named AgaCA233, from Catenovulum agarivorans DS-2 genome information through bioinformatics technology, the enzyme has high catalytic activity and thermal stability, and can be efficiently applied to the production of industrialized preparation of agar oligosaccharide. On the other hand, the gene engineering technology is used to the truncation mutation of the above agarase AgaCA233. The thermal stability and catalytic activity of the agarase AgaCA233 mutant of the application are greatly improved compared with the wild type AgaCA233, and the agarase is one of the most stable GH16 family agarases at present, and can be applied to the enzymatic industrial production of agar oligosaccharide, so as to greatly reduce the production cost of agar oligosaccharide.

Methods and systems are described that combine both genomic and epigenetic information to monitor neoantigen targets and molecular residual disease (MRD) in patients undergoing treatment with a personalized cancer vaccine (PCV). Also provided are neural networks trained to determine cancer recurrence in a patient treated with a PCV and methods for integrating a plurality of data types to identify disease specific signals in tissue and cell free DNA. Additionally, the disclosure provides genomic data integration methods including a variety of artificial intelligence (AI), machine learning, and deep learning methods to identify disease associated signals. These methods can elucidate molecular changes in the DNA sequence and epigenetic modifications in health and disease.

Methods, systems, apparatuses, devices, and computer program products are described. A system may use a rules engine and a reinforcement learning artificial intelligence (AI) model to recommend treatment options for a patient. In some examples, the AI model may be trained for a specific diagnosis. The system may receive patient information including the patient's diagnosis, genomic profile (e.g., partial or full genomic information), and treatment history. The system may input the genomic profile into the rules engine to determine any relevant treatment modifications for the user based on biomarkers in the genomic profile. The system may additionally input the patient information into the AI model to determine a set of treatment option recommendations and corresponding confidence metrics. The system may send the treatment option recommendations (e.g., which in some cases may be modified based on the output of the rules engine) to a user device for display.