115 results about "Phylogenetic tree" patented technology

The present invention relates to nucleic acid molecules which allow the identification of bacteria or groups of bacteria. For detection, the region of the bacterial genome containing the 23 S/5 S rRNA is used as the target sequence for the bacterial detection.

The invention provides a method for identifying predator nematophagous hyphomycete arthrobotrys through DNA bar codes and belongs to the field of fungus species identification. According to the method, RPB2 genes serve as target DNA bar code genes for identifying the predator nematophagous hyphomycete arthrobotrys, combined arthrobotrys sample experiment data and target fungus data merged strategy is adopted to establish a high-cavity database, meanwhile, RPB2 genes to be identified are compared with a gene library, an identifying rule is established based on a system generation tree method of genetic distance method and clustering analysis of the Kimura-2-parameter probability to identify species. The method has the advantages that the RPB2 genes serve as the DNA bar codes most suitable for identifying the nematophagous hyphomycete arthrobotrys, and the method is universal and easy to amplify and compare. The identifying efficiency and the reliability and accuracy of the identifying method are greatly superior to those of a conventional DNA bar code method, and the method makes up for the blank of the nematophagous hyphomycete arthrobotrys DNA bar code molecular markers and the method provides a useful research tool for researches on germplasm resource excavation, biocontrol application and genetic diversity of nematophagous hyphomycete.

The present invention permits identification of biological materials following recovery of DNA using standard techniques by comparing a mathematical characterization of the unknown sequence with the mathematical characterization of DNA sequences of known genera and species. The clinical identification of infectious organisms is required for accurate diagnosis and selection of antimicrobial therapeutics. The invention allows an ab initio approach with the potential for rapid identification of biological materials of unknown origin. The approach provides for identification and classification of emergent or new organisms without previous phenotypic identification. The technique may also be used in monitoring situations where the need exists for classification of material into broad categories of bacteria which could have an immediate impact on bio-terrorism prevention.

The invention provides a method, oligonucleotide and kit for detecting common high-risk HPV (human papilloma viruses). A fluorescence PCR (polymerase chain reaction) technology is adopted, HPV16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68, 26, 53, 66, 73 and 82 which possibly exist in a sample are subjected to initial detection and type identification. By the method, oligonucleotide and kit for detecting the common high-risk HPV, 18 high-risk types can be detected simultaneously, and the HPV 16 and 18 can be subjected to genetic typing simultaneously. On the basis of 18 types of high-risk HPV and affinity of other types on a phylogenetic tree, a high-risk HPV primer and a probe are designed, a background fluorescence value is reduced remarkably while detection accuracy, sensitivity and specificity are guaranteed, detection flux is increased remarkably, and detection cost is greatly reduced.

The invention relates to a mitochondria SNP (single nucleotide polymorphism) fluorescence-labeling multiple amplification kit capable of detecting 61 SNP loci at the same time. According to a mitochondria phylogenetic tree, based on genetic characteristics of Chinese populatio, 61 SNP loci which are high in polymorphism, low in mutation rate and strong in parting capacity are selected, wherein the 61 SNP lotuses comprise 54 loci in a coding region, 7 loci in a control region; the kit can be used for detecting the 61 SNP loci by virtue of specific primers. The kit which is used as a mitochondria detecting system is capable of carrying out amplification in three tubes at the same time and performing electrophoresis at the same time, so that haplotype diversity reaches 98.6%, and therefore, the mitochondria SNP fluorescence-labeling multiple amplification kit can be used as a kit for identifying the same maternal line, after autosome STR and Y chromosome STR.

The invention discloses a DNA bar code technology for identifying rosewood and rosewood products and an application method thereof. The technology is as below: constructing a high capacity database through a strategy by merging database of rosewood samples experiment data and a target plant; sequencing a DNA bar code sequence of the rosewood samples; merging the sequencing sequences with homologous sequences published in the Genbank database to construct a rosewood DNA bar code gene database with wide range of data sources; and establishing an algorithm and decision rules for the identification database by using matK+rbcL genes as the target DNA bar code gene for rosewood identification, and using a search tool method of a local alignment algorithm based on frequency, a genetic distance method based on Kimura-2-parameter probability and a phylogenetic tree method based on clustering analysis. The DNA bar code technology for identifying rosewood and rosewood products and the application method thereof establish an accurate and quick rosewood DNA bar code identification technology.

The invention relates to an equipment state overhaul management module for an EAM system of a power plant, which comprises a state monitoring point tracking submodule for obtaining detection data from state monitoring points, comparing the monitoring data with judgment conditions preset by the system and generating an exception report when exceptional data appear; a recording submodule used for recording the obtained detection data; and an overhaul item generating submodul used for generating the overhaul items of corresponding equipment when the detection data meet the set conditions. State overhaul is an equipment maintenance and management measure which tracks and analyzes the state monitoring points of the equipment and determines an equipment overhaul countermeasure according to a set overhaul policy in accordance with the comprehensive state of the equipment. The equipment uses a phylogenetic tree structure tissue for displaying, by collecting, analyzing and consulting exception information and variation trend data of relative state points, an equipment manager masters the equipment state in management range conveniently and an auxiliary decision tool for deciding the equipment overhaul countermeasure is provided.

A computer-implemented method and a computer system for identifying a phylogenetic tree from a plurality of biological sequences is provided. Each biological sequence is associated with a sampling date. First, the plurality of biological sequences is aligned and a distance matrix is obtained. Then, a subset of these sequences without any duplicated sequences is selected and a directed graph representation of the subset of biological sequences is generated based the associated sampling dates. Then, a minimum spanning tree is computed from the weighted directed graph representation. Then, in an iterative procedure, the sequences of unsampled evolutionary intermediates are inferred from mutation patterns that reflect the difference in sequence between the nodes in the minimum spanning tree. The new sequences are added with associated time stamps to the sequence set. Then, sets of identical sequences are removed. Then, an optimum branching is recomputed. This step is repeated until no new intermediates are found. In the final step, the sequences that have been set aside in the initializing step are added to the plurality of sequences derived in the update step. From this plurality of sequences an optimum branching is computed and identified as the phylogenetic tree. Amino acid changes repeatedly occurring on the internal branches of the obtained tree can be used to identify sequences and associated viral isolates suitable as vaccine strains for the following influenza season.

The invention relates to a preparation method for burkholderia cepacia, and an application in high-performance phosphate-dissolving microbial fertilizer by using the same. The method is characterized in that: the method comprises the following steps: (1) collecting deficient phosphorus soil for planting corns, putting the soil in a plastic bag, and placing the plastic bag in a 4 DEG C refrigerator for storing; (2) separating and screening a (burkholderia cepacia) strain; (3) detecting phosphorus solubilizing capability of the (burkholderia cepacia) strain; (4) identifying the strain: wherein the screened strain is subjected to a DNA sequencing and a 16SrRNA phylogenetic tree construction to be identified as the burkholderia cepacia. According the present invention, activation rate of the insoluble phosphate in the soil can reach to 10.94%-13.03%, utilization rate of the P reaches to 21.75%-37.98%, and the phosphorus fertilizer amount can be reduced by one third in application for the corns. The phosphate-dissolving microbial fertilizer provided by the present invention has advantages of low cost, good effect, disease resistance of plants enhancing, no pollution on environment and fully utilization of potential phosphorus resource.

The invention discloses a primer, kit and method for conducting genetic typing on the hantavirus by means of a PCR direct sequencing method. The primer comprises an upstream primer: ATTAGCCCWGTCATGAGTGT, and a downstream primer: CTTTGACTCYTTTGKYTCCA, wherein the Y is a C or a T, the W is an A or a T, and the K is a G or a T. The method comprises the steps of extracting a total RNA of a virus sample to be tested, conducting reverse transcription to obtain a cDNA, using the cDNA as a template, utilizing the primer for conducting PCR amplification, conducting sequencing on an amplified target fragment, constructing a phylogenetic tree by using corresponding fragments of known genotype representative strains as a reference on the basis of sequence information of the target fragment, and conducting the genetic typing on the virus sample to be tested according to the phylogenetic tree. When the primer is used, a specificity sequence of an S gene of the hantavirus can be obtained by only conducting one-time PCR amplification, and the genetic typing can be easily, conveniently and rapidly carried out on the hantavirus by utilizing the specificity sequence.

The invention discloses a pinus massoniana cpSSR polymorphism primer and an identification method of pine sibling species of the primer. According to design of a chloroplast genome of pinus massoniana, 16 pairs of cpSSR primers are obtained, further, 7 pairs of primers which are stable in difference and good in polymorphism are screened from the 16 pairs of cpSSR primers, and through utilization of the 7 pairs of primers, a finger print and phylogenetic tree of 8 kinds of pine sibling species are successfully established. Based on the 7 pairs of cpSSR primers, a PCR amplification reaction is carried out. Capillary electrophoresis technology is used to analyze a PCR product, 8 kinds of pine sibling species trees can be accurately identified. The primer and method are efficient, accurate, and convenient and are not prone to be affected by the environment. The polymorphism primer and an identification method thereof can reflect the genetic information of the 8 kinds of pine plasmons, andcan be used for research of identification of 8 kinds of pine sibling species and genetic relationship.

The invention relates to a phylogenetic tree construction method based on a sequence pattern mining algorithm. The phylogenetic tree construction method based on the sequence pattern mining algorithmcomprises the following steps: mining a specific pattern which is hidden in a sequence set and can be used for measuring sequence similarity to obtain an initial pattern set; filtering an unclosed frequent pattern in the initial patter set to acquire an optimized pattern set capable of representing the sequence set; and constructing a patter vector set and calculating the distance between numericvectors so as to construct a distance matrix for producing a phylogenetic tree. The sequence pattern which frequently appears in the sequence set is extracted by a sequence patter mining algorithm, the sequence set is converted into binary system by the filtered pattern set or the distance matrix is calculated in the form of giving weight information to the pattern vector set, and then the phylogenetic tree is constructed. For the large-scale and low-similarity sequence set, the more representative pattern in the sequence set can be mined by utilizing a pattern growth strategy, so that the extraction of a redundancy pattern which is useless for measuring sequence similarity is voided and measurement on the similarity among the sequences within the global range is optimized.

The invention relates to a PCV2d (porcine circovirus type 2) virus-like particle vaccine and a preparation method thereof. By means of epidemiological analysis for PCV2d strains of China, comparison of amino acid sequence information of a large quantity of collected strains as well as phylogenetic tree analysis, a Cap gene of a currently epidemic PCV2d strain in China is selected, PCV2d Cap protein is effectively expressed by an Escherichia coli prokaryotic expression system through codon sequence optimization, PCV2d virus-like particles are prepared successfully by purification and assembly in an in-vitro assembly and dialysis buffer solution, and form, size and concentration of the virus-like particles are not affected when the virus-like particles are placed for 6 months in a storage buffer solution at 4 DEG C and subzero 20 DEG C; the prepared PCV2d virus-like particle vaccine immunizes 21-day-old piglets, and a PCV2d challenge test proves that the vaccine has a good protecting effect for the piglets.

Selecting which sub-sequences in a database of nucleic acid such as 16S rRNA are highly characteristic of particular groupings of bacteria, microorganisms, fungi, etc. on a substantially phylogenetic tree. Also applicable to viruses comprising viral genomic RNA or DNA. A catalogue of highly characteristic sequences identified by this method is assembled to establish the genetic identity of an unknown organism. The characteristic sequences are used to design nucleic acid hybridization probes that include the characteristic sequence or its complement, or are derived from one or more characteristic sequences. A plurality of these characteristic sequences is used in hybridization to determine the phylogenetic tree position of the organism(s) in a sample. Those target organisms represented in the original sequence database and sufficient characteristic sequences can identify to the species or subspecies level. Oligonucleotide arrays of many probes are especially preferred. A hybridization signal can comprise fluorescence, chemiluminescence, or isotopic labeling, etc.; or sequences in a sample can be detected by direct means, e.g. mass spectrometry. The method's characteristic sequences can also be used to design specific PCR primers. The method uniquely identifies the phylogenetic affinity of an unknown organism without requiring prior knowledge of what is present in the sample. Even if the organism has not been previously encountered, the method still provides useful information about which phylogenetic tree bifurcation nodes encompass the organism.

The invention relates to a method for identifying Gaoyou duck varieties by utilizing molecular bioinformatics, belonging to the technical filed of biological variety identification. In the invention, the sequences of gene b of cytochrome of mitochondrial DNA of a Gaoyou duck and the duck variety to be tested are accurately obtained on the basis of gene cloning and DNA sequencing technologies, a plurality of bioinformatics software is utilized to accurately figure out the haplotype, variation locus, haplotype diversity, average nucleotide difference, nucleotide ramification degree, pure genetic distance, Kimura dual-parameter genetic distance among varieties, variety colony cluster result images and haplotype phylogenetic trees of each variety, and the genetic information difference among the varieties is utilized to identify the true and false of the Gaoyou duck varieties through software precise calculation and analysis results.

The invention is applicable to the technical field of biology, and provides a flora marker obtaining method and device, a terminal and a storage medium. The method comprises the following steps: obtaining flora sample data, wherein the flora sample data comprises abundance of N strain classification units in M flora samples, and N and M are positive integers; generating a phylogenetic tree by taking the N strain classification units as leaf nodes and taking the common ancestor of the J strain classification units in the N strain classification units as an intermediate node; and according to the direction from the root node to the leaf nodes, performing node search on the phylogenetic tree by utilizing a greedy algorithm to obtain at least one target node as the flora marker of the M florasamples. According to the scheme, the calculation complexity of high-dimensional flora sample data can be reduced, the target flora marker can be determined efficiently, and the calculation amount isreduced.

The invention relates to a method for identifying Japanese ginseng rhizomes and non-generic confusion or counterfeit species of the Japanese ginseng rhizomes based on ITS2, and discloses a method foridentifying the Japanese ginseng rhizomes and the non-generic confusion or counterfeit species of the Japanese ginseng rhizomes according to DNA (deoxyribonucleic acid) level. The method includes thesteps: 1) extracting Japanese ginseng rhizome DNA of a sample to be measured; 2) taking the DNA of the sample to be measured as a template and performing PCR (polymerase chain reaction) amplificationon fragments of an ITS2 sequence; 3) positively sequencing a PCR product and performing ITS2 database shearing to obtain the ITS2 sequences of the Japanese ginseng rhizomes; 4) building an NJ phylogenetic tree, analyzing intraspecific and interspecific average genetic distances and comparing secondary structural features. Results indicate that the ITS2 sequences of the Japanese ginseng rhizomes are clustered together, the intraspecific average genetic distances of the Japanese ginseng rhizomes are remarkably shorter than the interspecific average genetic distances of the non-generic confusionor counterfeit species of the Japanese ginseng rhizomes, secondary structures of the Japanese ginseng rhizomes widely differ from those of the non-generic confusion or counterfeit species, and the ITS2 sequences are used for rapidly and accurately identifying the Japanese ginseng rhizomes and the non-generic confusion or counterfeit species of the Japanese ginseng rhizomes. The method is simple tooperate, high in resolution ratio and strong in applicability and repeatability, and the Japanese ginseng rhizomes and the non-generic confusion or counterfeit species of the Japanese ginseng rhizomes can be rapidly and accurately identified.

Equine rhinovirus 1 (ERhV1) is a respiratory pathogen of horses which has an uncertain taxonomic status. The nucleotide sequence of the ERhV1 genome and amino acid sequence have been substantially determined (FIG. 2). The predicted polyprotein was encoded by 6,741 nucleotides and possessed a typical picornavirus proteolytic cleavage pattern, including a leader polypeptide. The genomic structure and predicted amino acid sequence of ERhV1 were more similar to those of foot-and-mouth disease viruses (FMDV), the only members of the aphthovirus genus, than other picornaviruses. Nucleotide sequences coding for the complete polyprotein, the polymerase, and VP1 were analyzed separately. The phylogenetic trees confirmed that ERhV1 was more closely related to aphthoviruses than to other picornaviruses. Virion proteins and virus-like particles are described and probes, primers, antigens, vectors, diagnostics and tests developed.

The invention discloses a method for isolating and identifying effective degrading fungi for corn stalks. The method includes: selecting samples, performing inoculated culture, screening and culturingthe fungi, through four screening and culturing mediums including a fungus screening and culturing medium, a Congo red cellulose screening and agar culturing medium, a seed culturing medium and an effective corn stalk degrading liquid state fermentation culturing medium, culturing the fungi obtained from multiple times of activation, preliminarily screening cellulose degrading fungi, observing growth form of the cellulose degrading fungi, performing molecular biological identification, subjecting fungus strains obtained from morphological identification to PCR (polymerase chain reaction) detection, and establishing a phylogenetic tree for obtained results so that to-be-tested fungus strains can be identified more correctly. The fungus screening and culturing medium is utilized to screen the effective corn stalk degrading fungi, and the Congo red cellulose screening and agar culturing medium, the seed culturing medium and the effective corn stalk degrading liquid state fermentation culturing medium are utilized to screen the effective degrading fungi. By utilizing different screening and culturing mediums to culture, the required fungi can be obtained more accurately, and accuracyof an experiment can be improved. Through strict sterilization during purification, identification results are enabled to be more accurate.

The invention provides a molecular method capable of identifying gynaikothrips ficorum and gynairothrips uzeli zimmerman. The molecular method comprises the following steps: (1) extracting DNA (Deoxyribose Nucleic Acid) of a sample to be identified; (2) taking the DNA extracted by the step (1) as a template, carrying out PCR (Polymerase Chain Reaction) amplification by using a primer pair and purifying an amplified product; (3) sequencing the PCR amplified product purified by the step (2), and accurately distinguishing two seeds through a basic group variation site, a genetic distance and a phylogenetic tree. The invention provides a method for identifying the gynaikothrips ficorum and the gynairothrips uzeli zimmerman through molecular biology; the method is simple to operate and accurate in identification and can be widely popularized.

The invention discloses a method for establishing a mycobacterium abscessus RUO database and a subtype super map. The method is characterized by including the following steps of mycobacterium abscessus strain collecting and DNA extracting; 2, gene library preparing and illumine HiSeq sequencing; 3, genome establishing and phylogenetic tree establishing; 4, sample preparing and strain detecting; 5, accuracy confirming. According to the method, mycobacterium abscessus subspecies are analyzed and determined; ionization-flight-time mass-spectrometric-detection subspecies information is desorbed in the mode that a matrix assists in laser, the RUO database and the established super map are established, the sensitivity and the specificity are detected through strain blind testing, the operation procedure and the diagnostic standard for subspecies-level laboratory identification are formulated, a work chain of the microbial standard in-vitro-diagnosis procedure is added, and the efficiency of all microbiological labs on mycobacterium abscessus subtype identification is improved.

The invention belongs to the technical field of plant molecular identification, and particularly relates to a strain identification method based on a dunaliella core gene sequence. The method mainly comprises the following steps: collecting, purifying and culturing a sample; extracting the DNA of the whole genome; constructing a DNA sequencing library; obtaining whole genome sequencing data of thealgae strain to be detected and the Dunaliella Quartolecta; screening and de novo assembly of sequencing fragments of the D. Quartolecta core genome are carried out, and genome segmentation, proteinfunction annotation and genome contig colinearity analysis are carried out on the assembled core genome sequence; constructing a phylogenetic tree by utilizing single nucleotide polymorphism, and whenan algae strain to be detected and Dunaliella Quartolecta are gathered into a cluster, the data support rate of branches is 0.99-1.00, the genetic similarity percentage is greater than or equal to 99%, and the algae strain to be detected is D.quartolecta.