399 results about "Genomic sequencing" patented technology

The invention relates to the technical field of virus whole genome sequencing, and discloses a method for virus whole genome sequencing, which comprises the following steps: S1, extracting a sample genome, operating according to a specification of a commodity kit, extracting RNA (Ribonucleic Acid) of the sample genome, and performing library construction after reverse transcription and targeted amplification. According to the method for sequencing the whole genome of the virus, the whole genome sequence of the virus can be obtained through the sequencing method, and compared with the current detection which only stays at negative and positive detection, the whole genome sequence can be obtained on the basis through the method for sequencing, epidemiological traceability is carried out, and meanwhile the sequencing cost can be effectively reduced.

The invention discloses bacillus velezensis Scm3 and application thereof.The bacillus velezensis Scm3 is obtained by screening a strain Scm with an inhibition effect on aeromonas hydrophila from turbot intestinal contents and then conducting ultraviolet mutagenesis on the strain to obtain a strain Scm3 with an enhanced antagonism effect on aeromonas hydrophila, and the strain Scm3 is applied to the preparation of the bacillus velezensis Scm3 and the application of the bacillus velezensis Scm3 to prepare the bacillus velezensis Scm3. 16SrDNA (deoxyribonucleic acid) sequence identification and genome sequencing prove that the strain is bacillus velezensis, and the inhibition mechanism of the bacillus velezensis Scm3 on aeromonas hydrophila is researched by a non-contact co-culture method.

The invention relates to a method for predicting river nitrogen metabolism gene abundance and key influence factors thereof based on automatic machine learning. Comprising the following steps: collecting a river water sample, detecting water quality physicochemical indexes, and performing metagenome sequencing to obtain nitrogen metabolism gene abundance; taking conventional water quality physicochemical indexes as explanatory variables, taking nitrogen metabolism gene abundance as a target variable, adopting automatic machine learning to construct a model, evaluating the performance of the model through a mean square error (MSE) and a fitting coefficient (R), and selecting an optimal algorithm for prediction; the model analyzes the relative contribution of each water quality index through an SHAP value graph, and reveals the relationship between each water quality index and gene abundance by using a partial dependency graph (PDP). The method shows high precision and good generalization performance in the aspect of predicting the abundance of the nitrogen metabolism gene, and is suitable for describing the nitrogen dynamic process of a river water body. The model can explain, analyze and quantify the influence of different water quality indexes on the nitrogen metabolism gene afterwards, and a scientific basis is provided for river water quality management and nitrogen metabolism optimization regulation and control.

The invention discloses a crested ibis habitat ecological quality trend analysis method and system, and relates to ecological quality monitoring. The method comprises the following steps: S1, constructing an intelligent sensing network, synchronously obtaining multi-source data of a habitat, identifying activity events of crested ibis, and generating a multi-dimensional habitat parameter table; s2, collecting environmental samples, and generating a microbial functional gene abundance matrix through metagenome sequencing and bioinformatics analysis; s3, taking the activity events of the crested ibis as behavior tags, and generating habitat function health indexes by coupling the parameter table and the matrix training machine learning prediction model; s4, performing spatial interpolation and trend analysis based on the habitat function health index to generate an ecological quality space-time evolution graph; and S5, based on the ecological quality space-time evolution graph, performing quantitative analysis by using a spatial differentiation statistical model, and generating a trend analysis report. By fusing multi-source data, real-time dynamic evaluation of habitat ecological quality and quantitative analysis of driving factors are realized, and a direct decision basis is provided for accurate protection.

The invention discloses a low-abundance pathogen detection method and system based on metagenome sequencing data, and belongs to the technical field of bioinformatics. The system comprises a species specificity sequence screening module (BactAlert2SSRs), a reference genome database construction module (BactAlert2Lib), a sequence alignment reference genome module (BactAlert2Map), a sequence alignment result analysis module (BactAlert2ID), and an SSRs posterior probability correction module (BactAlert2Rec). The detection system realizes efficient, accurate and reliable detection of low-abundance pathogens, and is suitable for analyzing third-generation metagenome sequencing data.

The invention relates to the technical field of bioinformatics data processing, in particular to a genome sequence compression method and system. The method comprises the following steps: acquiring genome sequencing data; comparing the sequencing data with a reference genome to determine a difference site; differentiating the difference sites as sequencing errors or real variations through a time sequence difference neural network model; performing differential compression coding according to an identification result; a friendly variation detection format is constructed, and rapid variation query is supported through a multi-level index structure and a variation metadata table. According to the method provided by the invention, the sequencing error and the real variation can be accurately distinguished through the time sequence differential neural network model, and important biological variation information is protected while the compression efficiency is improved by adopting the differential compression coding strategy.

The invention belongs to the technical field of genetic breeding, and particularly relates to a molecular marker for identifying sheep backfat thickness and application of the molecular marker, the nucleotide sequence of the molecular marker is shown as SEQ ID NO.1, and single nucleotide C-A mutation occurs at the 101bp site of the molecular marker. The molecular marker influencing the sheep backfat thickness is screened out through methods such as genome sequencing, variation site recognition, screening and annotation, whole genome association analysis and the like. By selecting sheep individuals with the genotype of CC as male parents or female parents, the backfat thickness of offspring can be reduced.

The invention discloses a flora regulation and control method and system for soil micro-ecology, and belongs to the technical field of microbial flora regulation and control, and the method comprises the steps: continuously collecting real-time environment data based on a target soil region, combining future climate prediction data, and generating a predicted scene sequence through Monte Carlo simulation; constructing a microbial community composition table, screening core strains, and performing metagenome sequencing; taking the core strain as a game participant, constructing a participant strategy set, calculating an income matrix library, setting an environment correction coefficient for each scene, carrying out scene-based game solving, and generating a balanced summary table; a regulation response prediction model is constructed, multiple optimization objectives are set, robustness constraints and expert rules are introduced, candidate regulation schemes are generated, optimal scheme solving is carried out, it is ensured that regulation measures can achieve an expected effect by guiding inter-species competition, and original flora balance is prevented from being damaged.

The invention relates to the technical field of breeding methods, in particular to a precise breeding method based on single nucleotide polymorphism, which comprises the following steps: carrying out whole genome sequencing and screening SNP (Single Nucleotide Polymorphism) markers related to target traits; designing a genotype detection chip based on the SNP marker, and performing genotyping; constructing a genetic evaluation model and predicting a breeding value; designing a matching scheme based on the breeding value; performing performance verification on the offspring and continuously improving the breeding strategy. By integrating whole genome sequencing, transcriptome and metabolome data and combining bioinformatics and an artificial intelligence algorithm, efficient screening of functional SNPs related to complex characters is achieved, and the problems of multi-character collaborative improvement and insufficient environmental adaptability in a traditional method are effectively solved.

The invention discloses a method for screening molecular markers based on apparent annotation information to carry out whole genome selective breeding, which comprises the following steps: step A, carrying out phenotype determination and genome sequencing on growth traits of a litopenaeus vannamei breeding population to obtain phenotype data and SNP (Single Nucleotide Polymorphism) typing data; step B, performing GS analysis by using phenotype data and SNP typing data, predicting a genome breeding value of a breeding population through a mainstream breeding model, and screening out an optimal breeding model; and step C, classifying chromatin states through ChromHMM analysis by combining the optimal breeding model with the key histone modified region, and screening out the functional SNPs with the key histone modified region. The SNPs have relatively strong functional relevance, are used for different regional groups, and can provide more accurate molecular markers for growth character genetic analysis of bred animals by using less SNPs under the same prediction accuracy, so that the accuracy of genetic breeding value estimation and the cross-group effect are remarkably improved, and the breeding process is accelerated.

The invention relates to the field of forensic medicine, and discloses a method and system for identifying smoking behaviors and application of the method and system. The construction method comprises the following steps: respectively obtaining saliva and excrement of a smoking object and a non-smoking object; performing metagenome sequencing to obtain original microbiome data; after processing the original microbiome data, extracting multi-omics feature information, including species information and gene function annotation information; based on a statistical analysis method, carrying out diversity analysis and screening microbial markers and functional genes significantly related to smoking behaviors; constructing a training set and a test set, and training a machine learning model and model evaluation by taking the microbial markers and / or the functional genes as input features; and performing smoking behavior identification on a target sample by using the model, and outputting a prediction result. The accuracy rate of model identification reaches 0.7966, the sensitivity is 0.8750, the specificity is 0.7037, and the method can be applied to health assessment and judicial expertise.

The invention relates to the technical field of medical care informatics, in particular to a respiratory infectious disease risk early warning method and system. The method comprises the following steps: acquiring a respiratory tract sample of a mutant virus infected person; the method comprises the following steps: extracting a mutant virus from a respiratory tract sample, carrying out genome sequencing on the mutant virus, positioning starting and ending positions of a spike protein coding gene in a genome by virtue of a biological information comparison method, extracting a spike protein coding sequence, and translating the spike protein coding sequence into an amino acid sequence; inputting the amino acid sequence into an immune escape prediction model to predict the immune escape score of the mutant virus; and performing risk assessment based on the immune escape score in combination with clinical monitoring information, and outputting a respiratory infectious disease risk early warning value. According to the invention, the risk of respiratory infectious diseases can be early warned better.

The invention relates to the field of plant breeding, and particularly provides a method for fixing rice heterosis by using an OsZFPP gene. The method comprises the following steps: firstly, constructing an OsZFPP1 gene or OsZFPP2 gene expression cassette driven by an OsECA1 promoter; then, an expression box of rice with three target points of OsPAIR1, OsREC8 and OsOSD1 being knocked out of CRISPR / Cas9 is constructed; integrating the expression cassette into the same vector to transform hybrid rice; screening three-gene homozygous mutation and OsZFPP positive plants, and identifying diploid cloned offspring through flow cytometry and genome sequencing. According to the method, the rice OsZFPP gene is combined with MiMe to provide a novel method for fixing the heterosis of the rice through apomixis, the heterosis of the rice can be successfully fixed through the method, an apomixis system with the high maturing rate can be obtained, and a novel solution is provided for fixing the heterosis of the rice through the apomixis.

The invention discloses methanogen lyase with the same protein family annotation as PeiR lyase and application of the methanogen lyase, and the methanogen lyase is obtained through homologous screening of Pfam protein family database annotation based on known PeiR lyase characteristics aiming at methanogen cell wall peptide bonds. The PeiR lyase protein can participate in the biological process of hydrolyzing archaea cell walls, methanogens are effectively killed, methane production is reduced, and the protein homologous with the protein has potential methane reduction potential. According to the invention, by integrating metagenome sequencing data of rumen microorganisms, screening methanogenic bacterium virus protein by using series bioinformatics software, and combining Pfam functional domain annotation to carry out homologous relationship analysis, a series of lyase is finally identified and is successfully expressed in a prokaryotic expression system, and meanwhile, an in-vitro gas production experiment result also shows that the methanogenic bacterium virus protein can be successfully expressed in a prokaryotic expression system. The crude enzyme liquid can significantly reduce the methane generation amount.

In various embodiments, the disclosure provides compositions, such as polypeptides, polynucleotides, gene editing systems, small molecules, vectors, or host cells, comprising and / or modulating the expression or activity of an immunomodulatory-related protein, such as a cytokine. In various embodiments, the disclosure also provides for the treatment of a disease or condition (e.g., a disease or disorder) using an agent comprising and / or modulating the expression or activity of an immunomodulatory-related protein. The present invention relates to methods for identifying such agents (e.g., diseases or conditions associated with whole genome association studies (GWAS), cancer genome maps (TCGA), whole genome sequencing, whole phenotype group association studies (PheWAS), expression quantitative trait locus (eQTL) studies, or combinations thereof), and methods for identifying such agents.

This invention relates to the field of medical testing, specifically to a set of biomarkers, reagent kits, and their applications for diagnosing hypertension in children. This invention involves collecting tongue / intestinal samples from obese children with hypertension, obese children, and healthy individuals, performing metagenomic sequencing, and statistically analyzing the sequencing data using bioinformatics to identify disease-related tongue / intestinal flora. By integrating tongue / intestinal flora with disease information, a combination of flora biomarkers is obtained. A binary classification prediction model constructed using this combination can maximally detect hypertension in obese children.

The invention belongs to the technical field of soil heavy metal pollution remediation, and discloses a heavy metal pollution soil bioremediation method and system based on soil metagenome sequencing, and the method comprises the following steps: carrying out gene sequencing on experimental microorganism class groups in heavy metal pollution soil to determine functional microorganisms containing heavy metal resistance genes; heavy metal resistant microorganism species in the soil can be accurately identified by judging whether functional genes are contained or not, and ecological unbalance possibly caused by blind introduction of alien species is avoided; a remediation strategy taking a microbial resistance mechanism as a core can effectively reduce the bioavailability of heavy metals in the soil, and also can improve the physicochemical properties of the soil through metabolic activity to form a sustainable remediation effect; the method has the advantages of being environmentally friendly, controllable in cost, lasting in effect and the like, and an innovative path is provided for soil ecological function restoration.

The invention discloses a fiveleaf virus GI.2 whole genome sequencing primer based on an amplicon sequencing technology and application thereof, and belongs to the technical field of virus gene sequencing. The primer group composed of 18 pairs of primers is preferably obtained according to an amplicon sequencing technology, the primer group can effectively improve the primer amplicon coverage degree, it is guaranteed that the primer amplicon coverage degree is 1.5-1.8 times that of a virus sequence, the amplification time is shortened, the amplification difficulty is reduced, the primer amplicon coverage degree and the whole genome capture efficiency are improved, and the primer amplification efficiency is improved. And the method has important significance on epidemic situation traceability and propagation trend of the fiveleaf virus GI.2.

The invention relates to the technical field of bioinformatics, in particular to an analysis method of pathogen metagenome sequencing data, the host background is greatly reduced through two-stage host filtering (especially ML fine filtering), and the detection capacity of low-abundance pathogens is greatly improved and the false negative rate is reduced by combining a low-abundance enhancement module (UMI / denoising); the dynamic database integration ensures that the coverage is wide and newest; a priority ranking algorithm is combined with clinical metadata, so that the ranking of real pathogenic bacteria is effectively improved, and the interference of non-pathogenic bacteria / contaminating bacteria is inhibited; the confidence evaluation of the low-abundance module reduces false positive; dynamically updated databases and intelligent sequencing effectively cope with the problems of new pathogens and incomplete databases, and missing detection is reduced; false detection is reduced through strict denoising, confidence evaluation and interpretation based on clinical rules.

The invention relates to the technical field of water ecological protection, in particular to a river type division method based on a small watershed water ecological environment protection stage. The method comprises the following steps: acquiring historical river water area data; obtaining a target watershed image by using a machine vision technology; performing water flow path analysis on the target watershed image to generate a water flow path network structure; carrying out biological sample collection on the target river, and carrying out genome sequencing treatment to generate biological genome data; performing memory information mining on the biological genome data to obtain watershed memory data; performing environmental transition correlation analysis on the watershed memory data to generate gene-environmental evolution data; performing drainage basin evolution trajectory reconstruction on the gene-environment evolution data based on historical river water area data to construct a drainage basin evolution trajectory; and performing drainage basin evolution form analysis on the water flow path network structure through the drainage basin evolution trajectory to generate drainage basin evolution form data. According to the method, efficient and accurate river division is realized.

The invention discloses a fingerprint spectrum of an oyster mushroom P2101 strain as well as a construction method and application of the fingerprint spectrum, and belongs to the field of oyster mushroom strain detection. The fingerprint spectrum is composed of 10 pairs of InDel markers developed on the basis of oyster mushroom whole genome sequencing. The InDel marker fingerprint spectrum of the oyster mushroom P2101 strain can be used for identifying the specificity of the oyster mushroom P2101 strain, has the advantages of short detection time, high accuracy and good repeatability, and has the specificity of the oyster mushroom P2101 strain in 48 collected oyster mushroom strains.

The invention belongs to the field of pleurotus eryngii strain detection, and particularly relates to a primer group for identifying the difference between pleurotus eryngii strains and application. In order to solve the problems that in the prior art, pleurotus eryngii strains are difficult to distinguish, and an existing method consumes too long time, the invention provides a primer group for identifying the difference between pleurotus eryngii strains and application, the primer group is composed of 9 pairs of InDel markers developed after pleurotus eryngii whole genome sequencing, according to the method, the identification time of the pleurotus eryngii strain is greatly shortened, the detection accuracy and repeatability are improved, and meanwhile the stability and universality of the method are guaranteed.

The invention provides a simplified genome sequencing library construction method and a kit and related application thereof. The construction method of the simplified genome sequencing library comprises the following steps: (1) respectively carrying out enzyme digestion on a plurality of DNA (Deoxyribonucleic Acid) samples by using restriction endonuclease; wherein restriction endonucleases adopted by all the samples are different from one another, and the tail ends of specific DNA fragments of the samples are generated to serve as sample bar codes of the samples; (2) mixing the enzyme digestion products of the samples, constructing a DNA library, carrying out fragment sorting on the DNA library, and taking the selected library as a simplified genome sequencing library; or carrying out fragment sorting on the enzyme digestion product of each sample, and carrying out DNA library construction by using the selected fragments to obtain the simplified genome sequencing library. According to the method, the experimental operation process is simplified, the library building efficiency is improved, and meanwhile, the feasibility of the restriction endonuclease for recognizing 6 basic groups based on a third-generation long-read-long sequencing platform in the simplified genome sequencing technology is also explored.

Apparatus and method of managing genomic sequencing data. In an embodiment, a data management controller is communicatively coupled to an external data repository over a communication network. The data management controller is configured to detect a first event triggering initial analysis on raw sequence data encoded in a standard file format and stored in the external data repository. The data management controller is configured to launch one or more analysis tools to perform the initial analysis on the raw sequence data stored in the external data repository, and to output initial analysis results. The data management controller is configured to determine whether the initial analysis results pass quality control, and control electronic storage of the raw sequence data when the initial analysis results pass quality control by storing the raw sequence data in archive storage, and deleting the raw sequence data from the external data repository.

The invention provides a composite standard substance aiming at animal pathogenic microorganisms and a preparation method and application thereof, the composite standard substance comprises microorganisms, and the microorganisms specifically comprise more than one bacteria, more than one fungi, more than one prokaryote, more than one protist and more than one virus. The pathogen classification family, genus and species of each microorganism in the composite standard substance are different; the nucleic acid concentration of any virus in the composite standard substance is greater than or equal to the nucleic acid concentration of any pathogenic microorganism in the non-virus microorganisms. The microorganisms in the composite standard substance cover five boundary classes of bacteria, fungi, prokaryotes, protists and viruses, and can meet quantitative / qualitative analysis or metagenome sequencing requirements of animal clinical pathogenic microorganism diversity; moreover, the composite standard substance disclosed by the invention is beneficial to ensuring that virus and non-virus microorganisms can be detected in one-time detection, and the possibility of false negative phenomenon when the total nucleic acid concentration of a sample is too low is reduced.

The present invention provides primers and methods for amplifying the entire genome of avian leukosis virus. The detection primer set for avian leukosis virus includes 18 pairs of amplification primers, the specific sequences of which are shown in SEQ ID NOs. 1 to 36. The detection primer set provided by the present invention can achieve relatively uniform coverage of avian leukosis virus, and in nanopore sequencing, 100% regional coverage of the genome is achieved. The method for preparing sequencing fragments of the entire genome of avian leukosis virus provided by the present invention is simple and easy to operate, with good amplification effect. Nanopore sequencing has the advantage of real-time analysis while sequencing, which can greatly shorten the detection time and can quickly identify and diagnose avian leukosis virus infection. At the same time, its entire genome sequence can be obtained. The obtained genome sequence can provide a scientific basis for virus tracing, pathogen mutation tracking, new strain identification and early warning, etc.

The invention relates to the technical field of microbiology, in particular to a biological reagent research and development method based on microbial functional gene screening. The method comprises the following steps: acquiring a microorganism sample, and performing genome sequencing extraction treatment and gene transcription analysis to generate transcriptome data of the microorganism sample; obtaining a biological reagent research and development target function, and performing target function gene screening treatment and gene targeted knockout treatment to generate a target function gene targeted knockout experimental group; carrying out gene cloning on the target functional gene targeted knockout experimental group, transferring into a preset host strain, carrying out function expression evaluation analysis to obtain a target functional expression level corresponding to each target functional targeted knockout gene, and carrying out excellent function screening and verification to generate a biological reagent excellent function verification gene, and the method is applied to a research and development process corresponding to a biological reagent so as to generate a target functional biological reagent product. The functional screening efficiency and the specificity of biological reagent products can be improved.

The invention discloses a genome sequencing sample processing method based on a microdissection technology. The method comprises the following steps: (1) preparing a paraffin section or a frozen section; (2) carrying out HE staining on the section obtained in the step (1); (3) carrying out laser microdissection on nucleic acid; (4) fragmenting the DNA sample, and treating a product obtained in the step (3) by utilizing an ultrasonication method to obtain a DNA fragment; a non-contact ultrasonic crusher is adopted, the power is 80%, ultrasonic treatment is carried out for 10 s, stopping is carried out for 20 s, and 15 cycles are carried out. And (5) carrying out on-machine pretreatment on the genome sequencing sample, wherein the treatment comprises tail end repair and joint connection treatment. According to the method disclosed by the invention, accurate cutting of the sample can be realized, a DNA sample is extracted from a very small amount of cells and a sample for sequencing is constructed, the sample can achieve the same or higher sequencing data quality as that of a traditional method, the usage amount of the cells is greatly reduced, and the repeatability of an experiment is improved.

The invention discloses a method for extracting DNA from marine sediments, and belongs to the technical field of DNA extraction. The method comprises the following steps: adding sodium hexametaphosphate and a cell lysis solution into the marine sediment, uniformly mixing, incubating and centrifuging to obtain supernate; adding a chloroform-isoamyl alcohol mixed solution into the supernate, uniformly mixing, centrifuging, and removing an organic phase to obtain a water phase; and adding linear polyacrylamide and sodium chloride into the water phase, uniformly mixing, adding ethanol, precipitating in a dark place, and centrifuging to obtain the DNA extract. Compared with the prior art, the method provided by the invention has the advantages that the DNA in the marine sediment can be effectively extracted, the extraction amount is high, the concentration is high, and the obtained DNA can better meet the metagenome sequencing requirement and the subsequent PCR reaction requirement.

The invention provides a large-scale chicken farm epidemic disease risk assessment method and system, and the method comprises the steps: setting a plurality of sampling points in a large-scale chicken farm, and collecting a corresponding microorganism sample at each sampling point; performing sample treatment and metagenome sequencing analysis on the microorganism sample to obtain pathogenic species and abundance information results corresponding to each sampling point; constructing a sampling point influence matrix, and determining a sampling point weight based on the sampling point influence matrix; determining the pathogen species and the pathogen nucleic acid abundance in the abundance information result, and performing assignment scoring on the corresponding pathogen based on the pathogen nucleic acid abundance to obtain a pathogen score; and determining a final risk score based on the sampling point weight and the pathogen score, and performing epidemic disease risk assessment of the large-scale chicken farm based on the final risk score. According to the method, the accuracy of risk assessment can be improved, a farm is helped to identify and assess potential epidemic disease risks, and targeted measures are taken to prevent epidemic diseases in the bud.