90 results about "Phylogenetic tree" patented technology

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.

An animal feed additive comprising a polypeptide having alkaline phosphatase activity is described, wherein the selected polypeptides have activity against relevant biological targets, are thermostable, and have high three-dimensional similarity to each other and to human intestinal alkaline phosphatase and close proximity on the phylogenetic tree.

The invention provides a phylogenetic tree construction method and system based on a nucleic acid sequence distance matrix, and the method comprises the steps: obtaining and processing original nucleic acid sequence data, and obtaining standard nucleic acid sequence data; extracting a plurality of nucleic acid sequences from the standard nucleic acid sequence data, obtaining a global alignment distance between any two nucleic acid sequences in the plurality of nucleic acid sequences, and generating an initial distance matrix of the standard nucleic acid sequence data; obtaining an overmetric deviation and a function of the initial distance matrix; iterative optimization is carried out on the initial distance matrix, and an optimized distance matrix with the minimum overmetric deviation and function is obtained; and constructing a phylogenetic tree based on the optimized distance matrix. An effective nucleic acid sequence distance matrix is obtained through a hybrid optimization technology, so that the phylogenetic tree can be accurately constructed under the condition that initial data is incomplete or the scale is too large.

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.

The invention belongs to the technical field of bioinformatics, and particularly relates to a method for screening cross-species HGT. The method comprises the steps of constructing a background database, inferring a homologous group, constructing a gene phylogenetic tree, inferring HGT based on the gene tree, inferring verification of candidate HGTs based on the gene tree, distributing the HGTs to a timeline and the like. According to the method, high-throughput and automatic screening of HGT events in a large number of gene datasets is realized by integrating a plurality of steps of phylogenetic analysis, sequence alignment, gene function annotation, statistical verification and the like. The method disclosed by the invention is particularly suitable for the HGT research of an ultra-long time length and an ultra-long evolution distance crossing a biological boundary, and an important scientific tool can be provided for understanding gene flow and function enhancement in a biological evolution process.

The invention belongs to the technical field of pathogen detection, and particularly relates to a primer group, a composition, a kit and a method for identifying apple edge rot pathogen based on qPCR (quantitative polymerase chain reaction). Comprising the following steps: constructing a polygene phylogenetic tree based on an ITS-LSU-TEF-TUB sequence, designing an apple edge rot pathogen sample and a primer probe, constructing a standard curve, carrying out PCR (Polymerase Chain Reaction) amplification detection on the apple edge rot pathogen, and judging a result according to the amplification curve after the reaction is finished. The detection method has good repeatability and stability, and compared with other detection technologies, fluorescent quantitative PCR has the advantages of being short in detection time, higher in detection sensitivity, higher in specificity, small in needed template amount, capable of effectively solving the PCR pollution problem, high in automation degree and the like.

The invention relates to the technical field of gene SNP molecular markers, in particular to a gene SNP molecular marker method and system for watermelon breeding, and the method comprises the following steps: respectively extracting DNA solutions of watermelon samples of a plurality of varieties, and performing fingerprint construction based on SNP typing; the method comprises the following steps: acquiring a 16S rRNA sequence of each watermelon flora, and dividing each 16S rRNA sequence into each base sequence; determining mutation associated parameters of each basic group; obtaining a transition probability matrix of each 16S rRNA sequence; correcting the sampling step length of each 16S rRNA sequence; the transition probability matrix is corrected; determining a feature vector of each 16S rRNA sequence; the genetic distance between the watermelon flora and the 16S rRNA sequence of the soil sample is determined, a phylogenetic tree is constructed, and the strongly correlated flora of the breeding environment of each variety of watermelon samples is determined. Therefore, the suitability of the watermelon breeding environment is improved.

The invention relates to the technical field of biology, and discloses an RNA (Ribonucleic Acid) evolution precursor screening method based on evolutionary biology and computational biology, which comprises the following steps: constructing a phylogenetic tree, screening an amino acid sequence, and predicting a three-dimensional structure of a dimer formed by bacterial transcriptase. Constructing a nucleotide analogue small molecule database; docking the predicted transcriptase dimer with a nucleoside analogue, and screening small molecules with an excellent binding mode; molecules similar to original nucleotide-protein interaction are screened out to serve as potential candidate molecules; and carrying out double-chain structure prediction on the screened candidate molecules to obtain the RNA small molecule evolution precursor. According to the method, nucleoside analogues are systematically screened out by combining evolutionary biology and computational biology methods to serve as precursor candidate small molecules of RNA in the RNA world, compared with a traditional RNA precursor experimental research method, the method is more systematic, and compared with life origin exploration purely based on evolutionary biology, theoretical result support of computational biology is provided.

The invention provides a cynaroides cynaroides chloroplast genome and application thereof, and belongs to the technical field of genes. The nucleotide sequence of the cynaros cynaroides chloroplast genome is shown as SEQ.ID.NO.1. The invention provides application of the cynaros cynaroides chloroplast genome in identification of cynaros cynaroides varieties and reconstruction of cynaros phylogenetic trees, and provides technical support for protection of cynaros cynaroides germplasm resources and species identification. According to the invention, the chloroplast genome of the cynaroides is used as a super DNA bar code for identifying the variety of the cynaroides, so that technical support is provided for protection of germplasm resources and species identification, and the application of the chloroplast genome of the cynaroides in variety identification and reconstruction of phylogenetic trees of the cynaroides is realized. The method is of great significance to plant breeding and genetic diversity evaluation, protection and utilization.

The present invention relates to the field of bioinformatics, and relates to a method for identifying variant sites that differentiate HPV risk levels, and a use thereof. The identifying method comprises: constructing a guide tree; constructing a phylogenetic tree; marking the phylogenetic tree; determining risk boundary points; performing risk distribution frequency analysis on variant sites; and performing screening to obtain variant sites that meet a preset distribution-frequency condition and variant genotype statuses, that is, characteristic variants for identifying high-risk HPV types. The method of the present invention is used to identify high-risk HPV types, so that large-scale rapid screening and detection based on single nucleotide sites can be achieved without sacrificing accuracy, thereby enabling rapid and precise prevention and control of high-risk HPV types.

The invention discloses a DNA bar code identification method for hypericum sampsonii hance and counterfeit products thereof, and belongs to the technical field of biology. The identification method comprises the following steps: taking DNA of a sample to be detected as a template, carrying out PCR amplification by using an ITS2 primer or a psbA-trnH primer, and carrying out sequencing and sequence splicing on an amplification product to obtain a DNA bar code of the sample to be detected. The amplification sequence is applied to construction of a hypericum phylogenetic tree or systematic analysis of the sequence, accurate identification of hypericum sampsonii hance is achieved, the identification method is simple, rapid, high in efficiency and good in repeatability, hypericum sampsonii hance, hypericum perforatum and other hypericum close-genetic plants can be accurately distinguished and identified, the identification effect is high, and the method is suitable for popularization and application. The identification success rate of hypericum sampsonii hance is greatly improved. The DNA barcode identification method provided by the invention lays a foundation for subsequent development of molecular biological detection technologies of hypericum sampsonii hance and counterfeit products thereof.

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.

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.

The invention discloses a directed evolution method for improving thermal stability of nitrilase, and belongs to the technical field of enzyme engineering. The ancestor enzyme with improved thermal stability is obtained by the following method: collecting a sequence of nitrilase, carrying out evolutionary tree analysis to obtain an evolutionary landscape, obtaining an amino acid sequence of the ancestor enzyme in combination with an ancestor enzyme reconstruction algorithm, and constructing an ancestor enzyme primary structure sequence library; predicting the tertiary structures of all ancestor enzymes to obtain a structural library; and finally, carrying out molecular dynamics simulation on all the ancestor enzyme tertiary structures to obtain a kinetic parameter library, and screening through specific kinetic parameters to obtain the novel heat-resistant ancestor nitrilase. And then predicting and verifying mutation sites, and screening out a forward mutant with improved thermal stability and enzyme activity.

The invention discloses a method for identifying rhizoma cibotii medicinal material base and adulterants thereof based on rbcL bar codes, and belongs to the technical field of medicinal material base molecular identification. The rbcL sequence of the rhizoma cibotii species is constructed by collecting rhizoma cibotii and adulterants thereof from different producing areas and combining the adulterants sequence downloaded from GenBank, K2P genetic distance analysis and phylogenetic tree construction are carried out based on the rbcL bar code, and it is determined that the rbcL is the optimal DNA bar code of rhizoma cibotii. The rbcL gene amplification primer is adopted to perform PCR amplification on the DNA sequence of the to-be-detected sample to obtain the corresponding sequence, the K2P genetic distance is analyzed and the phylogenetic tree is constructed according to the obtained sequence matrix, species can be obviously separated, the cibotium rhizome medicinal material and the source species of the adulterants can be clearly distinguished, and the method is simple and convenient to operate. A brand-new thought is provided for identification of the rhizoma cibotii medicinal material base and adulterants of the rhizoma cibotii medicinal material base, and the method has important significance for solving the problem of adulteration of rhizoma cibotii medicinal materials in the medicinal material

The present invention relates to the field of marine biology technology, and specifically to a method for analyzing food residues in the gastrointestinal tract of Antarctic krill using molecular sequencing technology. The method comprises the following steps: dissecting Antarctic krill in a low-temperature environment and obtaining total DNA and total RNA using a nucleic acid extraction kit, and amplifying target genes in combination with specific primer design; subsequently, barcode labeling and high-throughput sequencing library construction are performed, paired-end sequencing is performed using an Illumina NovaSeq platform, and data quality control and redundancy removal are completed to obtain high-quality sequence data, accurate species identification is performed based on multi-level sequence alignment and a lowest common ancestor algorithm, phylogenetic tree and network analysis methods are used to analyze the diversity and trophic level distribution of Antarctic krill food residues, and food sources are further traced through environmental DNA comparison. The present invention can significantly improve the accuracy and scope of species identification and is of great significance for understanding the energy flow and trophic level structure of the Antarctic ecosystem.

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.

The present invention first discloses the application of the chloroplast genome of *Cerasus serrula* var. *pubipetala* in variety identification and in reconstructing the phylogenetic tree of the subgenus *Cerasus*. The present invention uses the chloroplast genome of *Cerasus serrula* var. *pubipetala* as a super DNA barcode for identifying cherry blossom varieties, providing technical support for the protection of cherry blossom germplasm resources and species identification, and being of great significance for the breeding, genetic diversity evaluation, protection and utilization of plants in the subgenus *Cerasus*.

The invention belongs to the technical field of biocontrol bacteria, and particularly relates to pseudomonas mediterranei with a mildew-proof effect and application of the pseudomonas mediterranei. Specifically, a strain of Pseudomonas mediterranean with a potential biocontrol function is separated from rhizosphere soil of tobacco, and the strain of Pseudomonas mediterranean with the potential biocontrol function is separated from rhizosphere soil of tobacco. The full-length sequence of bacteria is obtained through 16S rRNA gene sequencing, and a phylogenetic tree is constructed to determine the taxonomic status and genetic relationship of the bacteria. A further research shows that the strain not only has a higher self-bacteriostasis rate, but also can inhibit the growth of aspergillus niger, aspergillus flavus, filamentous fungi and talaromyces varioti by generating volatile substances and fermentation products thereof. In addition, the bacteriostatic effect of the strain on the dried tobacco leaves is also verified, and the strain shows good application potential, so that the strain has wide application prospects.

The invention discloses a high-throughput genotype intelligent analysis method. The method comprises the steps of data acquisition and preprocessing, molecular marker recognition and genetic relationship and hybridization advantage prediction. Performing standardization processing on the high-throughput genotype data, establishing triple quality evaluation standards of coverage rate, conversion / transversing rate and error rate, and correcting batch effect through a position effect index; then calculating a genetic similarity matrix among the samples based on the preprocessed data, and analyzing and identifying a tag SNP with high centrality as a molecular marker through a linkage imbalance network; the markers are used for estimating the genetic relationship of the population and constructing a phylogenetic tree, and meanwhile, the hybridization advantage is predicted based on the relationship index of the heterozygosity and the genetic distance. According to the method, the genotype data quality is remarkably improved, molecular marker screening is optimized, the population genetic relationship is accurately estimated, the hybridization advantage is accurately predicted, and an efficient bioinformatics solution is provided for modern breeding.

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.

The present invention relates to the field of molecular biology and discloses a DNA barcode (clpP) for mosses and its applications. The DNA barcode (clpP) comprises a clpP gene fragment. The primer sequences for obtaining the DNA barcode (clpP) are shown in SEQ ID NOs. 1 and 2. The DNA barcode (clpP) is used to identify mosses and construct a phylogenetic tree of mosses. This technical solution overcomes the problems of poor versatility and low resolution of existing DNA barcodes for mosses.

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.

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.

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.

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.

The present invention discloses a chloroplast genome of Prunus variegata and its application in variety identification, wherein the nucleotide sequence of the chloroplast genome of Prunus variegata is shown as SEQ ID NO.1, and the chloroplast genome nucleotide sequence of the sample is compared with the chloroplast genome nucleotide sequence of Prunus variegata, and when the similarity index reaches above 99.9%, it is determined to be Prunus variegata; it can be seen that the chloroplast genome of Prunus variegata plays an important role in variety identification and in reconstructing a phylogenetic tree of the subgenus Cerasus; the present invention uses the chloroplast genome of Prunus variegata as a super DNA barcode to identify cherry varieties, provides technical support for the protection of cherry germplasm resources and species identification, and has important significance for the breeding of plants of the subgenus Cerasus as well as the evaluation, protection and utilization of genetic diversity.

The invention relates to the technical field of bioinformatics, and discloses a fungus multi-gene conjoint analysis method, system, equipment and medium. Target sequence data of a fungus sample to be identified are obtained, and an accurate sequence comparison reference library for each target marker gene is constructed in real time by using an original reference sequence; and accurate multi-sample multi-gene paired sequence comparison and sibling sequence acquisition are carried out to finally construct a multi-gene phylogenetic tree, so that comprehensive species identification is realized, and the accuracy and efficiency of species identification are remarkably improved. The method supports multi-sample accurate identification, does not need to predict the range of the sample family in advance, has expansibility of other biological groups, can realize rapid and accurate identification, can be widely applied to scenes with accurate and rapid identification requirements, and is high in practicability. The method comprises import and export pathogenic bacteria quarantine, food pathogenic bacteria monitoring, biological safety, production process of biological products and the like.

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.

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.