309 results about "Genomic sequencing" patented technology

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 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 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 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.

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 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 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 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 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 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.

The invention relates to a method for extracting genome DNA of plants rich in secondary metabolites and a buffer solution, and belongs to the technical field of molecular biology and botany. The method solves the technical problems of low DNA extraction efficiency, poor purity, easy degradation and the like when a traditional DNA extraction method is used for treating plant tissues rich in secondary metabolites such as alkaloid, polyphenol and the like. Comprising the following steps: adding a complexing agent such as polyethylene glycol or polyvinylpyrrolidone when grinding plant tissues in a liquid nitrogen environment; splitting by using a cell wall splitting buffer solution containing dithiothreitol and a nonionic surfactant; carrying out DNA release and extraction at 60-70 DEG C by adopting a CTAB (Cetyltrimethyl Ammonium Bromide) extraction buffer solution containing polyethylene glycol and papain; and then purifying and precipitating to obtain high-purity genome DNA (Deoxyribose Nucleic Acid). The method can effectively remove alkaloid, protein and other impurities, significantly improves the DNA yield and purity, and is suitable for genome sequencing, genetic resource protection, medicinal plant molecular identification and the like of plants with high secondary metabolites such as Stephania kwangsiensis and the like.

The invention relates to a computerized method for compressing genome sequencing data. The method comprises the following steps: comparing the genome sequencing data with reference sequencing data; obtaining one or more differential read sequences, each of the one or more differential read sequences being a read sequence of the genomic sequencing data that is different from a corresponding read sequence of the reference sequencing data; and obtaining compressed genomic sequencing data by compressing the one or more difference segment sequences using a statistical compression method or using an assembly method with a probabilistic data structure. In some embodiments, the method also has the step of assembling the plurality of reads to form reference data. In some embodiments, the method also has the step of storing the compressed genomic data in the blockchain.

The present application belongs to the technical field of enzyme engineering and plastic degradation, and particularly relates to an esterase, a preparation method thereof and application thereof in plastic degradation. Genome sequencing analysis is performed on a screened polyester plastic degrading strain, and an esterase 8GL004290 is successfully screened, which belongs to the alpha / beta hydrolase family. It is verified through experiments that the polyester degrading enzyme provided by the present application can not only degrade polyester model small molecule substrates, but also exhibits good degradation capacity for different polyester plastics. The esterase 8GL004290 has the highest degradation activity on a polyurethane substrate, and the substrate types are widely covered. Therefore, the present application has extremely important application value for the biodegradation treatment of mixed plastic waste.

The invention provides a large-scale cattle farm epidemic disease risk assessment method and system, and the method comprises the steps: setting a plurality of sampling points in a large-scale cattle 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; performing sample exception processing on the pathogenic species and the abundance information result to obtain a processing result; determining the pathogen nucleic acid abundance in the processing result, and performing assignment scoring on the corresponding pathogen based on the pathogen nucleic acid abundance to obtain a pathogen score; and carrying out epidemic disease risk assessment on the large-scale cattle farm based on the pathogen 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.

The invention provides a capture primer group and a kit for targeted Salivirus genome sequencing and application of the capture primer group and the kit, and belongs to the technical field of genome sequencing. The targeted capture primer group of the Salivirus virus genome comprises a primer 1 and a primer 2, the nucleotide sequence of the primer 1 is as shown in SEQ ID NO. 1, and the nucleotide sequence of the primer 2 is as shown in SEQ ID NO. 2. According to the invention, a universal reverse transcription oligo-T primer and the Salivirus specific primer group provided by the invention are put into the reverse transcription step at the same time, so that not only is a macro transcription effect achieved, but also a Salivirus sequence in a sample is synchronously identified for specific capture. According to the method, the complete Salivirus genome sequence can be efficiently obtained, and the method has good coverage and sequencing adaptability to the virus genome.

The application provides a kind of construction and application for sesbania sesban DNA fingerprint, belong to sesbania molecular marker technical field, the application is based on sesbania genome sequencing, first develops and screens out 8 pairs of SSR primers with sequence specificity and rich polymorphism, by analyzing the agarose gel electrophoresis result of PCR amplification product of SSR primer in different varieties, the assignment of different size, type of PCR amplification product is carried out, to form the DNA fingerprint of each sesbania, the application has the characteristics of easy operation, good repeatability, simple data processing, low cost and the like, and lays a foundation for the classification, identification and utilization of sesbania germplasm resources.

1. Name of the product of this design: the main body of the test kit. 2. Purpose of the product of this design: The kit and the main body of the kit can be used for sequencing operations, and are configured to contain one or more liquids, solutions, DNA, RNA, chemicals or other media and be used with an analytical unit for sequencing or biochemical analysis, wherein sequencing operations include genome sequencing, genome sequencing includes DNA or RNA sequencing, and other media include reagents. 3. The key point of the design of this product lies in its shape. 4. The picture or photo that best illustrates the design points: Stereoscopic drawing 1.

The present disclosure is in the field of low depth whole genome sequence and genetic sequencing. In particular, method of detecting contamination based on haplotype detection of the mitochondrial DNA.

The invention discloses a primer group and method for human metapneumovirus whole genome sequencing and application. Two groups of specific primer pools are designed for the metapneumovirus, totally comprise 21 primers, can effectively amplify the metapneumovirus type A and the metapneumovirus type B, are high in sensitivity and suitable for multi-platform detection, and provide a new direction for detection, typing, traceability and evolutionary analysis of the metapneumovirus.

This invention provides a chalcone isopentenyltransferase gene. GiPT16 This invention relates to the GiPT16 protein, amplification primer set, and applications, belonging to the field of biogenetics technology. It is based on *Glycyrrhiza inflata* (GiPT16 protein, amplification primer set, and applications). Glycyrrhiza inflata Using whole-genome sequencing data and a reverse genetics strategy, the key aromatic isopentenyltransferase GiPT16, involved in the isopentenylation modification of chalcone active ingredients, was successfully identified and functionally characterized. This enzyme was confirmed to specifically catalyze the biosynthesis of psoralen and glycyrrhizin C using DMAPP as a donor. It is the first chalcone isopentenyltransferase characterized in *Glycyrrhiza inflata*, filling a gap in the study of key enzymes in the chalcone isopentenylation metabolic pathway of this species and providing important evidence for further elucidating the molecular mechanisms of quality formation in *Glycyrrhiza inflata* medicinal materials.

This invention discloses methanogenic lyases with the same protein family annotation as PeiR lyases and their applications. These enzymes are obtained through homology screening based on the known characteristics of PeiR lyases targeting peptide bonds in the methanogenic cell wall, using the Pfam protein family database annotation. PeiR lyase proteins participate in the biological process of hydrolyzing archaea cell walls, effectively killing methanogens and reducing methane production. Proteins homologous to this protein have potential methane-reducing potential. This invention integrates rumen microbial metagenomic sequencing data, uses a series of bioinformatics software to screen methanogenic viral proteins, and combines Pfam functional domain annotation for homology analysis, ultimately identifying a series of lyases. These lyases were successfully expressed in a prokaryotic expression system, and in vitro gas production experiments also showed that the crude enzyme solution significantly reduced methane production.

This invention provides a precise quantitative sequencing method based on multi-level atomic structure internal standards, belonging to the field of quantitative metagenomic sequencing technology. The invention first constructs a multi-level atomic structure internal standard system containing at least two concentration levels of internal standard plasmids, forming multiple statistical response units within the same concentration level. After adding the internal standard plasmids to the nucleic acid of the sample, library construction and sequencing are performed. The sequencing signals of the target gene and statistical response units are statistically analyzed, sequencing response parameters are calculated, and consistency analysis is performed on multiple statistical response units within the same concentration level to determine the dynamic limit of detection (LOQ) and to determine the validity of the target gene quantification results. This invention can dynamically determine the LOQ under the current experimental conditions, improving the reliability of quantification results for low-abundance targets.

1. Name of the product in this design: Sequencing instrument and sequencing instrument body. 2. Intended use of this design: The sequencer can be used for sequencing operations and is configured for use with analytical units for sequencing or biochemical analysis, including genome sequencing, such as DNA or RNA sequencing. The cassette can be configured to contain one or more liquids, solutions, DNA, RNA, chemicals, or other media, including reagents. 3. The key design feature of this product is its shape. 4. The image or photograph that best illustrates the design's key points: Design 1, 3D view 1. 5. Design 1 is designated as the basic design.

The invention relates to a primer set for whole genome sequencing of chlamydia psittaci, the primer set comprises a primer subset p1 and a primer subset p2, the primer subset p1 comprises primers with sequences as shown in SEQ ID NO: 1-240, and the primer subset p2 comprises primers with sequences as shown in SEQ ID NO: 241-480. The primer group disclosed by the invention not only can accurately obtain the whole genome sequence of chlamydia psittaci, but also is adaptive to the sequencing modes of all second-generation and third-generation sequencing platforms.

The present invention provides a donor-recipient matching model for enterobacteria transplantation and a method for constructing the same. By combining donor and recipient information, the donor-recipient matching model is successfully constructed through metagenomic sequencing, meta-analysis, and neural network modeling. The model is applied to clinical experiments for performance comparison and evaluation of the reliability of the model, verifying the feasibility of the model prepared by the present invention and can be successfully applied to the treatment of gynecological diseases.

This invention relates to the field of medical technology, specifically to a method for preoperative risk assessment and prediction in liver transplant patients with hepatocellular carcinoma, comprising the following steps: Sample collection: selecting plasma samples and corresponding clinicopathological information from liver transplant recipients of hepatocellular carcinoma, and clarifying the inclusion and exclusion criteria for samples; Plasma cell-free DNA extraction and whole-genome sequencing: extracting and quality-controlling cell-free DNA from the plasma samples collected in step S1, constructing a sequencing library, and performing low-coverage whole-genome sequencing. This invention utilizes plasma-extracted cfDNA for whole-genome sequencing, combined with clinical testing information, to construct a preoperative risk assessment and prediction model for postoperative recurrence in liver transplant recipients of hepatocellular carcinoma based on non-invasive testing. This model can be used to predict the probability of recurrence-free survival before liver transplantation. The model derivation cohort integrates clinical records and circulating tumor DNA data for preoperative recurrence risk prediction.

The invention relates to the technical field of forest tree hybridization, and discloses a forest tree hybridization parent precise matching method based on multi-omics analysis, which comprises the following steps: S1, obtaining multi-omics data: performing genome sequencing, transcriptome analysis, proteomics analysis and metabonomics analysis on forest tree population individuals; a plurality of omics data such as genetic variation sites, gene expression quantity, protein expression abundance and metabolite spectrums are obtained. According to the forest tree cross parent accurate matching method based on multi-omics analysis, forest tree genetic characteristics are analyzed comprehensively through multi-omics data, genomics, transcriptomics, proteomics and metabonomics data are deeply fused, genetic factors closely associated with target traits are accurately identified, and the accuracy of forest tree cross parent matching is improved. According to the method, the scientificity of parent matching in forest tree cross breeding on the molecular level is remarkably improved, the fuzziness and uncertainty of traditional judgment only according to phenotype and experience are abandoned from the source, the parent matching accuracy is greatly improved, and the breeding work is more targeted and efficient.