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51 results about "Phylogenetic tree" patented technology

A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the evolutionary relationships among various biological species or other entities—their phylogeny (/faɪˈlɒdʒəni/)—based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry.

Automatic analysis system for land utilization flow change in land change investigation

The invention relates to the field of geographic information technology and natural resource management, and discloses an automatic analysis system for land utilization flow change in land change investigation. The system comprises an object-level spatiotemporal spectrum tree reconstruction and data initialization module, a topological potential energy field construction module based on evolution entropy, a multi-scale geometric difference extraction and morphological analysis module, a variable stiffness topological adsorption and decoupling module based on a stiffness ratio, and a flow damping filtering and event serialization module driven by semantic rules. The system constructs a topological potential energy field by using a historical state vector and semantic stiffness, performs one-way adsorption, adjustment or retention on a difference polygon according to relative stiffness, and cleans invalid traffic based on a damping matrix. According to the method, through physical field simulation and semantic logic verification, high-frequency disturbance misjudgment is effectively eliminated, pattern spot boundary correction is ensured to conform to the legal weight, and the authenticity and logic self-consistency of change survey data are improved.
Owner:CHINA GEOLOGICAL SURVEY MILITARY-CIVILIAN INTEGRATED GEOLOGICAL SURVEY CENT

Hepatitis E virus rapid detection method and system based on animal detection technology

The invention relates to the technical field of molecular biology, and discloses a hepatitis E virus rapid detection method and system based on an animal detection technology, and the method comprises the following steps: carrying out nucleic acid extraction on a hepatitis E virus sample to obtain a nucleic acid extraction sample; establishing a PCR system of the nucleic acid extraction sample, and generating uniform microdroplets of the nucleic acid extraction sample and the PCR system; calculating a rupture coefficient of the uniform microdroplet, performing PCR amplification on the uniform microdroplet to obtain an amplified microdroplet, and performing signal detection on the amplified microdroplet by using a preset fluorescent dual-channel to obtain a fluorescent detection signal; generating a two-dimensional scatter diagram of the amplified droplets to determine FAM positive droplets in the amplified droplets; and analyzing the HEV genotype and variation site of the hepatitis E virus sample to establish an HEV strain evolutionary tree and risk-inducing factors of the hepatitis E virus sample, and generating an HEV geographical distribution heat map of the to-be-detected region by combining the HEV strain evolutionary tree and the risk-inducing factors. According to the invention, the accuracy of rapid detection of hepatitis E virus can be improved.
Owner:东莞市中堂镇农业技术服务中心(东莞市中堂镇畜牧兽医站东莞市中堂镇动物卫生监督所东莞市中堂镇粮所)

A high-throughput genotype intelligent analysis method

ActiveCN120656541BBiostatisticsProteomicsGenetic linkage disequilibriumGenetics
The application discloses a high-throughput genotype intelligent analysis method, which comprises data acquisition and preprocessing, molecular marker identification and prediction of genetic relationship and hybridization advantage; high-throughput genotype data are subjected to standardization treatment, three quality evaluation standards of coverage, transversion / transversion ratio and error rate are established, and batch effect is corrected through a position effect index; then genetic similarity matrix between samples is calculated based on the pretreated data, a label SNP with high centrality is identified as a molecular marker through linkage disequilibrium network analysis; the population genetic relationship is estimated by using the marker, and a phylogenetic tree is constructed, and the hybridization advantage is predicted based on the relationship index of heterozygosity and genetic distance. The application significantly improves the quality of genotype data, optimizes the screening of molecular markers, accurately estimates the population genetic relationship and accurately predicts the hybridization advantage, and provides an efficient bioinformatics solution for modern breeding.
Owner:INSTITUTE OF CROP SCIENCE CHINESE ACADEMY OF AGRICULTURAL SCIENCES +1

System and method for transmission timeline generation

According to an example aspect of the present invention, there is provided a method for generating a transmission timeline, the method comprising: determining, based on SNP information, SNP evolutionary distance from a reference genome for each sample; determining, based on the SNP information, SNP evolutionary distance between each sample; and generating, based on: the SNP information, the SNP evolutionary distances from the reference genome, the SNP evolutionary distance between the samples, the mutation rate, generation rules and the corresponding timestamps; a dated phylogenetic tree, said tree comprising sample nodes) and non-sample nodes, wherein each sample may correspond to a node, for example.
Owner:SOLU HEALTHCARE OY

An end-to-end method and related equipment for constructing B-cell clonal lineage forests

This application provides an end-to-end method and related equipment for constructing a B-cell clonal lineage forest, applicable to the field of data processing technology. This application identifies the first test Fv sequence corresponding to each receptor sequencing sequence by performing germline alignment on multiple acquired receptor sequencing sequences, and generates a germline Fv sequence corresponding to each receptor sequencing sequence. Then, the first test Fv sequences are filtered for integrity and further classified into several first clonal type sets. Based on these second clonal type sets and the same-type class conversion probability, corresponding first phylogenetic trees are constructed to form a first lineage forest. Node optimization is performed on all first phylogenetic trees. After confirming that the same-type class conversion probability meets preset requirements after updating all second phylogenetic trees, all second phylogenetic trees are visualized, thereby improving the efficiency of relevant personnel's systematic understanding of adaptive immune response mechanisms.
Owner:广州赛业百沐生物科技有限公司

Methods and systems for probabilistic typing of microbial strains

The present invention relates to a microbiological typing method comprising providing: a database of genetic profiles of microbial strains; and a phylogenetic tree, assigning the genetic spectrum to a location in the phylogenetic tree, and assigning a frequency of variation of the spectrum in the tree. The microbial typing comprises the following steps: measuring genetic spectrums of the microorganisms, determining the variation probability of each genetic spectrum in a database relative to the measured genetic spectrums, and calculating the variation probability according to the variation frequency; and determining that the microorganism belongs to a classification unit of the tree if at least the probability of the classification unit is above a threshold. According to the invention, the phylogenetic tree is constructed from the core genome of the microbial species and a predefined set of genetic markers is selected from the auxiliary genome of the microbial species.
Owner:BIOMERIEUX SA

Measurement method of sexual reproduction animal germline mutation rate and application

The invention provides a method for measuring the mutation rate of a sexual reproduction animal whole genome level nucleotide germline. The method comprises the following steps: (1) performing genome sequencing on a to-be-detected species to obtain sequences of all coding proteins of the to-be-detected species; (2) constructing a phylogenetic tree of a to-be-tested species; (3) obtaining the divergence time Tdivergence between the species to be detected and the sibling species; (4) optimizing the phylogenetic tree of the species to be tested; and (5) obtaining the annual germline mutation rate [mu] year of the species to be detected. The principle of the method is as follows: neutral regions or neutral sites are widely distributed in a genome, and mutations generated at the positions are generally not influenced by natural selection; the mutation rate of the germline can be calculated by analyzing the change of the variation frequency of the sites along with time. The method provided by the invention not only is widely applicable to sexual reproduction animal species with obtained genome or transcriptome data, but also is accurate and efficient, fills up the blank of the prior art, and has great significance in theoretical research and practical application of biomedical engineering.
Owner:OCEAN UNIV OF CHINA

A crop disease prevention and control method and system for improving the efficiency of pesticide use

The present application relates to the technical field of crop disease prevention and control, more specifically, to a crop disease prevention and control method and system for improving pesticide use efficiency, soil samples and plant samples are collected, wherein the soil samples and plant samples come from different growth areas and environments, and different growth stages; the microbiome in the soil samples and plant samples is extracted, and the DNA of the microorganisms is extracted; the total DNA of the microorganisms is subjected to high-throughput metagenomic sequencing to obtain sequencing data; according to the sequencing data, a bioinformatics analysis method is used to identify pathogenic bacteria in the microbial community and drug-resistant genes existing in the pathogenic bacteria; a phylogenetic tree of the microbial community is constructed to analyze the succession relationship of the pathogenic bacteria; the pesticide resistance characteristics and change trend of the pathogen are analyzed; according to the analysis results of the microbial phylogenetic tree and the drug-resistant genes, disease prevention and control suggestions are generated to guide the selection and use of pesticides in the disease prevention and control process, greatly reducing the amount of pesticides used and improving the efficiency of disease prevention and control.
Owner:FRUIT TREE INST OF CHINESE ACAD OF AGRI SCI

Construction method of plasmid propagation risk prediction model

The invention provides a construction method of a plasmid propagation risk prediction model. The construction method of the plasmid propagation risk prediction model comprises the following steps: constructing a plasmid network community; constructing a strain evolutionary tree; and based on the plasmid network community and the strain evolutionary tree, constructing a plasmid propagation risk prediction model to evaluate and classify the plasmids and output the categories of the plasmids. According to the method, a plasmid propagation risk assessment classification framework based on a plasmid network community and a strain phylogenetic tree is constructed, and the problem that in the prior art, the propagation risk of plasmids is judged only through the similarity of plasmid sequences, but the propagation mode and the evolutionary relationship of the plasmids in a strain population are ignored is solved.
Owner:ICDC CHINA CDC

Human haplogroup hierarchical tracking and macro haplogroup normalization method

The invention discloses a human haplogroup hierarchical tracking and macro haplogroup normalization method, and relates to the field of group genetics and bioinformatics software methods. Comprising the following steps: establishing an adjacency list data structure based on an authoritative phylogenetic tree; constructing a synonym normalization dictionary for processing the heterogeneity problem of haplogroup naming; a hierarchical path backtracking algorithm is realized, backtracking is performed from a target haplogroup node to a root node based on a depth-first search principle, a complete evolutionary path is generated, the hierarchical path backtracking algorithm comprises a path integrity verification mechanism, a broken path or a circular reference error is automatically detected and reported, and the biological rationality of the generated path is ensured; a path output interface is provided, and a positive-sequence path representation mode and a negative-sequence path representation mode are supported. The method has the advantages of being high in standardization degree, high in automation level, high in reproducibility, good in universality and good in user experience.
Owner:CHONGQING MEDICAL UNIVERSITY

Training group efficient construction method for waxy corn whole genome selective breeding

The invention discloses a training group efficient construction method for waxy corn whole genome selective breeding. The method comprises the following steps: widely collecting common inbred lines or DH lines or inbred lines or DH lines subjected to genetic improvement in waxy corn breeding; carrying out phylogenetic tree, population structure and pedigree analysis on the collected waxy corn inbred line or DH line; dividing the inbred line or the DH line into a plurality of heterosis groups based on a phylogenetic tree, pedigree information and a group structure analysis result; respectively selecting a plurality of representative inbred lines from the heterosis groups; preparing a plurality of hybrids from a plurality of representative inbred lines or DH lines by adopting a sparse part dicolumn hybridization design method among different heterosis groups; performing multi-environment planting identification on the plurality of hybrids to obtain a plurality of character data; predicting phenotypes of all possible hybrids assembled by a plurality of representative inbred lines; the general combining ability effect of each representative inbred line or DH line is estimated through the predicted phenotype of the hybrid, and parent inbred line materials with high general combining ability are screened out. The method solves the problem that the predictability of newly introduced germplasm or germplasm with relatively far genetic relationship is reduced due to the fact that a training group used in the existing waxy corn whole genome selective breeding only contains a hybrid combination of a few backbone inbred lines and lacks representativeness.
Owner:INST OF AGRI SCI ALONG YANGTZE RIVER IN JIANGSU

Phylogenetic tree construction method and system based on deep learning and beam search

This invention discloses a phylogenetic tree construction method and system based on deep learning and beam search. It predefines evolutionary scenarios, setting evolutionary parameters for each scenario with reference to real-world biological sequence attributes. Training, validation, and test sets are created based on simulated phylogenetic trees and corresponding multiple sequence alignment data according to the predefined parameters. A deep learning classifier with convolutional neural networks and long short-term memory neural networks as its core is constructed. The deep learning classifier is trained and validated using the training and validation sets, and its accuracy is tested using the test set. Based on the trained deep learning classifier and the sliding window method, classification predictions are performed on all sub-quad-sequence trees of the four-sequence data. A phylogenetic tree reconstruction is performed on the multiple sequence data using an improved stepwise addition method and the quad-sequence tree classification prediction results, resulting in a complete reconstruction. This enables phylogenetic tree construction under conditions of different species numbers and sequence lengths.
Owner:CHINESE INST FOR BRAIN RES BEIJING +1

Novel bacterium with electrogenesis function and application thereof

The invention discloses a novel bacterium with an electrogenesis function and application thereof, and belongs to the technical field of microbial technology and biological energy. According to the invention, a novel strain with stable electricity generation capability is screened from papermaking wastewater in the final discharge phase of a microbial fuel cell (MFC). The homology between the 16s rRNA gene sequence of the bacterial strain and the known bacterial strain of Cupriavidus pauculus is the highest. The Cupriavidus pauculus PMWA1-3 strain is determined to be a new strain of Cupriavidus in combination with a phylogenetic tree construction result, and the new strain is named as Cupriavidus pauculus PMWA1-3. The bacterial strain can grow by taking a phenol organic pollutant catechol as a unique carbon source, and when the bacterial strain is used for constructing an MFC (Microbial Fuel Cell), the highest power generation voltage is 291.7 mV, and the maximum power density reaches 202.2 mW / m, which indicates that the bacterial strain has strong power generation capability.
Owner:SHANDONG AGRICULTURAL UNIVERSITY

Bacillus cereus strain and application thereof

The invention discloses a bacillus cereus strain and application thereof, a phylogenetic tree is constructed through whole genome sequencing according to housekeeping genes, the phylogenetic tree is determined to belong to bacillus cereus (Bacillus cereus), and the preservation number is CGMCC (China General Microbiological Culture Collection Center) No.34800. The strain B2 obtained through separation can secrete indoleacetic acid (IAA), IAA serves as auxin and is beneficial for stimulating plant root development and promoting root growth, so that the water and nutrient absorption capacity of plants is enhanced, the adaptability of the plants in a stress environment is improved, meanwhile, the strain B2 can regulate and control sodium and potassium ion transport in pepper plants, and the yield of the pepper plants is increased. Specifically, the expression level of the key ion transporter gene in the pepper is up-regulated. The bacillus cereus strain B2 is an efficient microbial resource and can be used for developing a microbial inoculant or a biological fertilizer so as to promote growth of crops such as capsicum in salinized soil, improve the salt resistance of the crops and guarantee and improve the sustainable production capacity of capsicum in the salinized soil.
Owner:HENAN AGRICULTURAL UNIVERSITY

Streptomyces strain for producing purpurin, streptomyces liquid and application of streptomyces liquid

The invention belongs to the technical field of microbial resources and natural pigment production, and particularly relates to a streptomyces strain for producing purpurin, a streptomyces liquid and application thereof, the streptomyces strain is XS01-03Na, the preservation number is CGMCC No.35420, and the streptomyces strain is preserved in China General Microbiological Culture Collection Center on July 28, 2025. By means of sequencing, multi-site sequence comparison, phylogenetic tree construction and the like, the XS01-03Na disclosed by the invention is found to be a new strain of streptomycete; meanwhile, the XS01-03Na disclosed by the invention has the characteristic of high yield of purpurin, and the produced purpurin has excellent stability and antibacterial activity and can be applied to various fields such as printing and dyeing, food processing, medicine and health care and the like.
Owner:ZHEJIANG WANLI UNIV

A visualization method for epidemic virus field based on spatiotemporal trajectory data

This invention belongs to the field of infectious disease prevention technology, specifically relating to a method for visualizing infectious disease virus fields based on spatiotemporal trajectory data. The method includes: collecting multi-dimensional data related to infectious diseases, including spatiotemporal trajectory correlation data, virus detection data, and patient-related data (based on data from children with diarrhea at Tianjin Children's Hospital from July 2020 to August 2023); cleaning, standardizing, coding, and statistically analyzing the data; constructing a spatiotemporal distribution field, a genotype distribution field, and a risk correlation field based on a spatiotemporal axis; and visually presenting the data using a combination of various charts such as bar charts, line charts, statistical tables, and phylogenetic trees, combined with an interactive interface. This method integrates multi-source data to accurately display the spatiotemporal epidemic characteristics of infectious diseases, the evolutionary patterns of viral genotype distribution, and the correlation between genotypes and patient characteristics. All results are based on measured data, providing scientific support for infectious disease prevention, control, and treatment, and improving the efficiency and accuracy of data application.
Owner:TIANJIN CHILDRENS HOSPITAL

Ultrahigh-precision AI variety identification system and adaptive optimization method thereof

The invention discloses an ultrahigh-precision AI variety identification system and an adaptive optimization method thereof, and the method comprises the steps: obtaining a high-quality tag data set, carrying out the preprocessing, obtaining a tag data matrix, carrying out the dimension reduction processing through PCA and singular value decomposition, determining a tag reduction set, and carrying out the recognition of the tag reduction set. Three machine learning algorithms of Random Forest, XGBoost and LightGBM are combined with cross validation and Bayesian optimization to screen a final marker, a final model is trained through a random forest, and ultrahigh-precision identification of varieties is realized through multiple test voting and phylogenetic tree auxiliary correction. The method can solve the problems of long identification period, low accuracy, tedious operation and the like in a traditional variety identification method, effectively improves the variety identification efficiency and accuracy, reduces various costs, and can be widely applied to the fields of agriculture, gardening, ecology and the like.
Owner:TIANJIN BIAOHUAXING GENE TECH CO LTD

A method, system, device, and medium for fungal multi-gene joint analysis

The present application relates to the technical field of bioinformatics, and discloses a kind of fungal multi-gene joint analysis method, system, equipment and medium, the present application obtains the target sequence data of the fungus sample to be identified, utilizes original reference sequence to construct accurate sequence alignment reference library for each target marker gene in real time, and carries out accurate multi-sample multi-gene paired sequence alignment and close sequence acquisition, finally constructs multi-gene phylogenetic tree, realizes comprehensive species identification, significantly improves the accuracy and efficiency of species identification.The present application supports multi-sample accurate identification, does not need to know the sample genus range in advance, and has the expandability of other biological groups, can realize rapid and accurate identification, so that it can be more widely applied in scenes with accurate and rapid identification requirements, such as import and export pathogenic bacteria quarantine, food pathogenic bacteria monitoring, biological safety and biological product production process.
Owner:INST OF MICROBIOLOGY CHINESE ACAD OF SCI

Function annotation abundance sequence-based base model training method and device

The invention relates to a base model training method and device based on a functional annotation abundance sequence. The method comprises the following steps: S1, carrying out function annotation on an open reading frame of a genome or metagenome sample; s2, counting the occurrence frequency of each annotation and constructing a sequence according to an abundance descending order; s3, after the sequence is subjected to token processing, inputting the sequence into a model based on Transform, and adopting joint training of language modeling, comparative learning and classification loss to obtain species-level and token-level fixed dimension embedding; s4, on the basis of the embedding, completing downstream tasks such as phylogenetic tree construction, species identification and phenotype prediction, BGC / MGC recognition and key gene positioning in three levels, namely a genome level, a gene cluster level and a gene / protein level. In the embodiment of the invention, good uniformity, expandability and interpretability are displayed, and the dependence on a reference database is reduced. The corresponding device comprises a data processing module, a model training module and an application module, and can be realized by program instructions in a computer readable storage medium.
Owner:ZHEJIANG LAB

Analysis method for revealing provenance and diffusion of tropical plants based on chloroplast genome

The invention provides an analysis method for revealing provenance and diffusion of tropical plants based on chloroplast genomes, and relates to the technical field of plant analysis, and the analysis method comprises the following steps: obtaining unuploaded complete chloroplast genome data of a to-be-analyzed plant; annotating a chloroplast genome sequence and checking an annotation result by taking the to-be-analyzed plant chloroplast genome uploaded with the NCBI as a reference; performing sequence alignment on the whole genome of the chloroplast, and identifying homologous regions and evolutionary variation; performing sequence comparison on the chloroplast genome of the plant to be analyzed and the chloroplast whole genome of the foreign group species, and constructing a phylogenetic tree; constructing a time tree by using the ancient fossil nodes of the plant to be analyzed; collecting modern distribution area data of plants to be analyzed, and performing ancestor area reconstruction analysis by adopting different models; the binarization characteristics of'source 'and'sink' of regional effects are expanded, and the biological region combination is innovated according to the immigration and emigration rates of species and is divided into a radiation region, an incubation region, a corridor region and an accumulation region.
Owner:QINGDAO UNIV OF SCI & TECH

Method for separating and screening fungi on surface of koji-covered straw

PendingCN121991805ADiverse environmental toleranceEnvironmental adaptability guaranteeFungiComponent separationBiotechnologyMolecular identification
The invention relates to a method for separating and screening fungi on the surface of koji-covered straw in the technical field of biological separation, which comprises the following steps: S1, taking a koji-covered straw sample, adding sterile normal saline, oscillating to fully disperse microorganisms, preparing a bacterial suspension mother solution, and carrying out gradient dilution to obtain bacterial suspensions with different concentrations; s2, separation and purification: coating a rose-bengal culture medium with the bacterial suspensions with different concentrations, carrying out inverted culture, picking single colonies, and inoculating the single colonies to a new rose-bengal flat plate for purification; and S3, molecular identification: extracting the purified strain genome DNA, carrying out PCR amplification by using fungus universal primers ITS1 and ITS4, sequencing a PCR product, carrying out BLAST comparison with an NCBI database, constructing a phylogenetic tree, and determining the strain species. According to the scheme, the fungus strain with specific functional characteristics for white spirit processing is obtained.
Owner:MOUTAI INST

Primer pair for identifying coptis chinensis species, identification method and application thereof

The invention provides a primer pair for identifying coptis chinensis species, an identification method and application thereof, and belongs to the technical field of molecular identification. The primer pair for identifying the coptis chinensis species comprises an upstream primer and a downstream primer, the nucleotide sequence of the upstream primer is as shown in SEQ ID NO.1, and the nucleotide sequence of the downstream primer is as shown in SEQ ID NO.2. Specific primers are designed aiming at coptis chloroplast ycf1 genes, target fragments can be accurately amplified, sequences obtained based on amplification of the primers can be used for constructing phylogenetic trees, and then the seven species of coptis chinensis, coptis triangularis, coptis omeiensis, coptis wuzhi, coptis yunnanensis, coptis short calyx and coptis japonica can be clearly distinguished. The identification method provided by the invention is simple and convenient in steps, is not limited by plant growth stages and sample forms, does not need complex equipment, and is convenient to popularize in laboratories and grassroots institutions. And molecular level evidence can be provided for rhizoma coptidis classification and resource protection.
Owner:CHONGQING ACAD OF CHINESE MATERIA MEDICA

Application of euonymus grandiflorus chloroplast genome and euonymus grandiflorus species identification method

The invention discloses application of a euonymus grandiflorus chloroplast genome and an euonymus grandiflorus species identification method, and belongs to the technical field of gene detection and analysis. The invention discloses a complete euonymus macranthus chloroplast genome for the first time, the complete euonymus macranthus chloroplast genome is formed by sequentially splicing 25 continuous nucleotide fragments as shown in SEQ ID NO. 1 to SEQ ID NO. 25, the evolutionary status of the complete euonymus macranthus chloroplast genome in euonymus genus is analyzed through a phylogenomics method, and a molecular basis is provided for taxonomic dispute of the genus species. The molecular identification technology based on chloroplast genome nucleotide sequence comparison can efficiently distinguish the euonymus myrianthus and related species, and breaks through the limitation of traditional morphological identification. Besides, by constructing a multi-species phylogenetic tree of the euonymus, the phylogenetic position of the euonymus grandiflorus is defined, and a genomics basis is provided for genetic diversity research, germplasm resource protection and cross breeding of plants of the euonymus.
Owner:WEIFANG MEDICAL UNIV

SNP (Single Nucleotide Polymorphism) site set for accurately identifying germplasm resources of down producing goats and special chip thereof

The invention discloses an SNP (Single Nucleotide Polymorphism) site set for accurately identifying germplasm resources of down producing goats and a special chip thereof, and belongs to the technical field of molecular genetic breeding. The SNP locus set comprises 10,000 differential SNP loci, is obtained by screening whole genome re-sequencing data of 43 individuals of Inner Mongolia down producing goats (Alba type and Arabic type), Liaoning down producing goats, southern Xinjiang down producing goats and northwest Tibetan white down producing goats, and is clear in chromosome distribution, suballele frequency and functional region. According to the special liquid chip prepared on the basis of the site set, the probe length is 120 bp, the design conforms to specific parameters, the average detection rate of samples and sites exceeds 99% when the sequencing depth is larger than 5 *, five cashmere goat varieties can be accurately distinguished through principal component analysis and phylogenetic tree construction, and technical support is provided for germplasm resource protection, breeding improvement and germplasm innovation of the cashmere goats.
Owner:INNER MONGOLIA AGRICULTURAL UNIVERSITY

Bar code and identification method for identifying phoebe wood

The invention belongs to the technical field of phoebe wood identification, and relates to a bar code for identifying phoebe wood and an identification method, the bar code comprises a rpl32-trnLUAG bar code, a ycf1 bar code and a rpl32-trnLUAG + ycf1 combined bar code, the sequence of the rpl32-trnLUAG + ycf1 combined bar code is shown as SEQ ID NO.5-9, the rpl32-trnLUAG + ycf1 combined bar code is used for identifying phoebe zhennan, phoebe tenuifolia, phoebe bournei, phoebe sheareri and phoebe chekiangensis in phoebe, and the primer sequence of the rpl32-trnLUAG + ycf1 combined bar code is shown as SEQ ID The method for identifying the phoebe wood adopts the rpl32-trnLUAG and ycf1 bar codes, and identifies phoebe zhennan, phoebe bournei, phoebe sheareri and phoebe zhejiangensis in the phoebe on the basis of SeqMan software and a phylogenetic evolutionary tree method. The bar code for identifying the phoebe wood, provided by the invention, has richer sequence information sites, so that the species identification capability is improved, and accurate identification of five types of phoebe wood with extremely close structural characteristics is realized.
Owner:ZHEJIANG ACAD OF SCI & TECH FOR INSPECTION & QUARANTINE +1

A rapid detection kit for coxsackie virus a16 gene subtypes

The application discloses a coxsackievirus A16 gene subtype detection kit, which comprises three groups of primer probe combinations and can be used for simultaneously detecting three different gene subtypes (B1a, B1b and B1c) of coxsackievirus A16. Compared with a traditional gene sequencing and phylogenetic tree analysis method, the kit has high throughput, high specificity and high sensitivity in detection of coxsackievirus A16 genotype, and can be used for enterovirus monitoring and prevention of potential extensive infection and disease burden of coxsackievirus A16.
Owner:JIANGSU PROVINCIAL CENTER FOR DISEASE CONTROL AND PREVENTION (PUBLIC HEALTH RESEARCH INSTITUTE OF JIANGSU PROVINCE)

Methods and systems for probabilistic typing of microbial strains

The present invention relates to a microbiological typing method comprising providing a database of genetic profiles of microbial strains, a phylogenetic tree, assigning the genetic profiles into locations in the phylogenetic tree, and a frequency of variation of the profiles in the tree. The microbial typing comprises the following steps: measuring genetic spectrums of the microorganisms, determining the mutation probability of each genetic spectrum in a database relative to the measured genetic spectrums, and calculating the mutation probability according to the mutation frequency of a predefined hierarchy of a phylogenetic tree; and determining that the microorganism belongs to one of the groups of microorganisms if the group reaches an identification performance criterion, the criterion being reached if at least one probability of variation of the group is greater than a first predefined threshold.
Owner:BIOMERIEUX SA

Analysis method and analysis system for automatically processing metagenome high-throughput sequencing data binning to obtain viral genome and application

PendingCN121096424AEnsemble learningBiostatisticsOriginal dataSequence clustering
The invention discloses an analysis method for automatically processing metagenome high-throughput sequencing data binning to obtain a viral genome, which comprises the following steps: acquiring second-generation sequencing original data, and performing data quality control to obtain Reads to be analyzed; a plurality of Reads are assembled into an overlapping group through overlapping of fragments, statistics is conducted on the overlapping group, and a length distribution diagram is drawn; reconstructing a viral genome based on contig binning, and generating a box after sequence clustering; constructing a three-dimensional matrix of all boxes according to the attributes of the sequence, and predicting and identifying the species category of each box; carrying out quality identification on the virus box bin, and detecting and rejecting virus host genes; counting the abundance of the virus box bin in each sample to generate a virus box bin abundance table; constructing a virus annotation database, completing species annotation, constructing a virus evolutionary tree, and finally generating a report. The invention further discloses an analysis system and application for implementing the analysis method.
Owner:SHANGHAI OE BIOTECH CO LTD

Method and apparatus for accelerating large phylogenetic trees

This invention discloses an accelerated method and apparatus for visualizing large phylogenetic trees. The method includes: acquiring the attributes of all nodes in the phylogenetic tree; clustering the leaf nodes of the phylogenetic tree based on horizontal and vertical coordinates to obtain outliers and node clusters; if all descendant leaf nodes of a node belong to one of the node clusters, and the number of descendant leaf nodes is not less than a certain threshold, then treating the node as a new leaf node and setting the visibility state of the descendant leaf nodes to invisible, thereby obtaining a new phylogenetic tree; for the new phylogenetic tree, determining whether each leaf branch is invisible due to being covered by other nodes, and acquiring the visibility state of each node in that leaf branch to generate the accelerated result of the phylogenetic tree. This invention avoids the phenomenon of clustering and collapsing when visualizing large phylogenetic trees.
Owner:COMP NETWORK INFORMATION CENT CHINESE ACADEMY OF SCI

Screening method of high-temperature yeast for producing ester in yeast for making hard liquor

PendingCN121450446AFungiMicrobiological testing/measurementBiotechnologyColony morphology
The screening method comprises the following steps: S1, sample treatment: taking a high-temperature yeast sample, adding sterile water, oscillating and uniformly mixing, and then carrying out gradient dilution; s2, primary screening: coating a PDA culture medium with the diluent, and separating and purifying yeast strains through colonial morphology observation and microscopic morphology observation after constant-temperature culture; s3, secondary screening: inoculating the purified yeast strain to a tributyrin solid culture medium, performing constant-temperature culture, and screening out a strain with relatively high ester production capacity according to the size of a transparent circle around a bacterial colony; s4, molecular biological identification: constructing a clear strain taxonomic status through sequence alignment and phylogenetic tree construction; and S5, fermentation condition optimization: determining key influence factors through a single factor test, and optimizing fermentation conditions by adopting a response surface test to obtain optimal ester production fermentation parameters. According to the method, high-efficiency screening and fermentation condition optimization of the high-yield ester yeast in the high-temperature yeast for making hard liquor are realized through targeted screening and accurate identification.
Owner:MOUTAI INST