47 results about "Genome database" patented technology

The invention relates to the technical field of bioinformatics, in particular to a gene pool data retrieval method and system and a storage medium. The method comprises the following steps: acquiring multi-source genome data, performing quality control on the multi-source genome data based on an FAIR principle, and performing efficient storage and indexing by utilizing a distributed storage system so as to obtain a distributed genome database; performing cross-species homology analysis on the distributed genome database, and constructing a multi-level evolutionary tree model, so as to obtain evolutionary relationship map data; mapping gene structures and functions among different species according to the evolutionary relationship map data so as to obtain cross-species gene mapping data; receiving retrieval query data input by a user; and performing query type identification on the retrieval query data to obtain optimized query data. Through the multilevel evolutionary tree model and cross-species gene mapping, gene function comparison and prediction among different species are realized.

The present invention discloses a method and system for designing primers for sequencing targeted pathogenic microorganisms, the method comprising the following steps: step 1) obtaining genome data of pathogenic microorganisms and establishing a pathogenic microorganism genome database; step 2) obtaining the conserved regions of pathogenic microorganisms according to the pathogenic microorganism genome database; step 3) designing multiple primers according to the conserved regions in step 2); step 4) evaluating the specificity and inclusiveness of the multiple primers designed in step 3), and selecting multiple primers with specificity and inclusiveness of ≥90%. The primer set obtained in the present invention can detect multiple strains of pathogens at the same time, and the primer detection results are more accurate than those obtained in the prior art.

The invention discloses a construction method and application of a pathogenic microorganism genome database. The method comprises the steps of genome acquisition, genome screening, target region grabbing, strain verification, target region sequence clustering, redundancy elimination and database merging. The construction method of the pathogenic microorganism genome database is suitable for targeted high-throughput sequencing, and the corresponding amplification relationship between the primer and the corresponding microorganism genome sequence is obtained through the operations of screening, filtering, simulation amplification and the like on pathogenic microorganism genome data; the risk of wrong identification of pathogenic species can be reduced by constraining the corresponding relationship.

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

The invention relates to the technical field of biological genetic engineering, in particular to application of a brassica napus BnaA01G0331000ZS gene in drought stress resistance. The BnaA01G0331000ZS gene is cloned by using cDNA of double 11 leaves as a template through a sequence published in a brassica napus genome database, an over-expression vector is constructed and genetically transformed into rape variety high oil for transgenic function verification, the drought resistance of the obtained over-expression transgenic line is obviously enhanced compared with that of a wild type, and the BnaA01G0331000ZS gene has the advantages that the BnaA01G0331000ZS gene is obtained; therefore, the gene can positively regulate the drought stress resistance of the rape. Therefore, the invention provides a new gene resource for adversity stress resistance of rape.

The invention provides a pathogen detection method based on targeted high-throughput sequencing. The pathogen detection method comprises the following steps: S1, acquiring NGS original sequencing data of a pathogen sample to be detected and a negative control sample; s2, removing low-quality data from the obtained original sequencing data, then performing host sequence filtering, and finally performing plasmid sequence filtering to obtain high-quality sequencing Read; s3, comparing the pathogen reference genomes to obtain specific Read data; s4, performing classification according to a comparison result, and calculating the specific Read number and the RPM value of each pathogen; s5, constructing a microbial reference genome database, and verifying the species specificity of the specific Read in the NT database; and S6, grading pathogen detection signals in the to-be-detected sample according to the RPM value and the NTRPM value to obtain a result. The method provided by the invention can effectively reduce false positive of a detection result and interference of background signals, the detection result is accurate, and the method can be well applied to the fields of disease diagnosis, epidemiological investigation, public health prevention and control and the like.

The invention relates to the technical field of construction of genome databases, in particular to a construction method of a pathogenic microorganism genome database. The method comprises the following steps: carrying out pathogen characteristic point location analysis on a pathogen microorganism genome sequence to obtain pathogen characteristic point location data; carrying out physiological and biochemical characteristic analysis on a pathogenic microorganism genome sequence according to the pathogenic characteristic point data, carrying out genome evolution relation simulation, and then carrying out prepositive relation linkage identification to obtain prepositive relation linkage data; performing relation nested structure analysis on the prepositive relation linkage data, and performing relation coding index construction to obtain a linkage relation coding index; and carrying out dynamic retrieval condition matching on the linkage relationship coding index, and carrying out genome database construction to obtain the pathogenic microorganism genome database. The construction technology of the genome database is improved, so that the construction technology of the genome database is more perfect.

The invention discloses a disease-resistant application of an arabidopsis thaliana AtRTP7 gene. The invention relates to application of inhibiting the expression of an arabidopsis thaliana AtRTP7 gene in enhancing the resistance of plants to pathogenic bacteria. The number of the arabidopsis thaliana AtRTP7 gene in an arabidopsis thaliana genome database is AT4G02820. The invention focuses on the S gene AtRTP7 of arabidopsis thaliana, the growth phenotype of the mutant is observed, and inoculation experiment is carried out on the mutant by using sclerotinia sclerotiorum and botrytis cinerea. The result shows that the growth of the AtRTP7 mutant is not obviously influenced, the AtRTP7 mutant shows obvious resistance to sclerotinia sclerotiorum and botrytis cinerea, and the scab area and the pathogenic bacterium biomass of the AtRTP7 mutant are obviously lower than those of a wild plant. Therefore, the S gene AtRTP7 of arabidopsis thaliana can be used as a potential gene resource for green prevention and control of sclerotinia rot of colza.

The invention provides application of a potato StMYB4 gene in regulation and control of solanine accumulation in potato tubers, the StMYB4 gene is cloned through a sequence published in a potato genome database by taking cDNA of leaves of cultivated species Hubei potato No.3 and AC142 as a template, an overexpression and knockout vector is constructed, genetic transformation is performed on the Hubei potato No.3 and AC142 respectively for transgenic function verification, and the solanine accumulation in the potato tubers is regulated and controlled. It is found that excessive StMYB4 genes can significantly promote synthesis of solanine in potato tubers, and knockout of the StMYB4 genes can significantly inhibit synthesis of solanine in potato tubers. The application of the potato StMYB4 gene to regulation and control of tuber solanine can be used for molecular marker development and low solanine variety breeding.

A method of constructing a microbial identification database, the method comprising: (ST02) acquiring genome data for microorganisms from a genome database; (ST06) determining whether a criterion is satisfied by the genome data thus acquired; (ST16) for respective sets of the genome data that were determined that they satisfied the criterion, predicting proteins to be expressed; and (ST20A, 20C) constructing a mass-to-charge ratio database including mass-to-charge ratio lists, the mass-to-charge ratio lists being predicted for the respective sets of the genome data based on the proteins thus predicted.

The invention provides a probe design method for improving the detection performance of a gene chip, and belongs to the technical field of DNA and RNA microarrays. Comprising the following steps: S1, downloading a genome sequence of a target detection species; s2, downloading a whole genome database of bacteria, fungi, animals, plants and viruses, and classifying according to species; s3, performing multi-sequence alignment on the whole genome data of each species; and S4, analyzing the comparison result of the genomic sequences of the to-be-detected species, and carrying out sequence conservative machine calculation to obtain the conservative properties of different genomic sequences of the same species. By optimizing the position relation of the probes on the chip, the detection performance of the DNA and RNA microarray can be remarkably improved, and the specific method comprises rectangular, linear and discrete layout of the probes, distribution of repeated probes and multi-probe design. The methods can improve the accuracy, sensitivity and reliability of detection, and provide data with higher quality for pathogenic microorganism identification.

The invention relates to the technical field of oat breeding, and discloses a molecular marker related to the content of neutral detergent fibers in oat, a primer combination and application, the molecular marker is an insertion deletion (PAV) marker, the PAV molecular marker is located at a 5D chromosome of an oat reference genome, the physical position is 5D: 424169687, and 161bp deletion is achieved; the national genome database login number of the oat reference genome is GWHGDJH00000000.1, and the national genome database login number of the oat reference genome is According to the molecular marker related to the content of the neutral detergent fibers in the oats, the primer combination and the application, detection can be carried out in the seedling stage of the oats by adopting the molecular marker and the detection method, the breeding period is remarkably shortened, the breeding efficiency is improved, and the breeding cost is reduced; meanwhile, a PCR primer combination designed on the basis of the molecular marker is high in specificity and accuracy, can be used for predicting and screening the neutral detergent fiber content of the feeding oat and is used for genetic breeding of the oat.

A method of constructing a microbial identification database, the method comprising: (ST02) acquiring genome data for microorganisms from a genome database; (ST06) determining whether a criterion is satisfied by the genome data thus acquired; (ST16) for respective sets of the genome data that were determined that they satisfied the criterion, predicting proteins to be expressed; and (ST20A, 20C) constructing a mass-to-charge ratio database including mass-to-charge ratio lists, the mass-to-charge ratio lists being predicted for the respective sets of the genome data based on the proteins thus predicted.

The invention discloses a microbial community identification method and system, and particularly relates to the technical field of microbiomics. A hidden Markov model database constructed on the basis of multiple types of ribosome RNA sequences is adopted for global search, a huge whole genome database in the prior art is replaced, and the size of the database is reduced; moreover, the hypervariable region sequence is extracted from the identified ribosome RNA sequence in a targeted manner, and the extracted sequence data and the quality information in the original sequencing data are pasted back, so that the hypervariable region sequence file containing the complete quality information is generated. The sequence data contains sequence information for identification, and a ribosome RNA marker gene sequence can be accurately identified and extracted from metagenome or metatranscriptome sequencing data; the original sequencing data can be used for a traditional amplicon analysis process, and can also support downstream deep analysis, so that seamless connection with the traditional amplicon analysis process is realized.

The invention belongs to the technical field of molecular biology, and particularly relates to a molecular marker for identifying genetic sex of different populations of micropterus salmoides as well as a primer pair and application of the molecular marker. The invention provides a molecular marker for identifying genetic sex of different populations of micropterus salmoides. The molecular marker is located between the 35054224th site and the 35054476th site of a micropterus salmoides genome database ASM2243578v1 genetic sex number 15 linkage group. The used primer pair comprises M-F and M-R. PCR amplification is carried out through the primer pair, if two bands of 307 bp and 253 bp are obtained through amplification, the male is determined, and if only the band of 253 bp is determined, the female is determined. According to the method, the sex of the largemouth bass can be accurately identified, a result can be obtained on the same day, and the repeatability is high. The method lays a technical foundation for sex control breeding and unisexual breeding of the micropterus salmoides.

The invention discloses a chlamydia psittaci cgMLST molecular typing method, and belongs to the field of microbial molecular typing and tracing. According to the invention, an operation technology for carrying out molecular typing on chlamydia psittaci by using a core genome multi-site sequence typing system (cgMLST) is established for the first time. The chlamydia psittaci cgMLST system is established through the processes of collecting chlamydia psittaci genomes in a disclosed genome database, obtaining core genomes through quality control screening and generic genome analysis, screening core genes suitable for typing under multiple screening conditions and the like. And comparing with a phylogenetic analysis result based on core genome SNP difference to confirm the resolution and reliability of the typing system. According to the typing technology, the core genome of the chlamydia psittaci is determined for the first time, and the typing technology can be used for molecular typing and epidemiological monitoring of the chlamydia psittaci.

The invention belongs to the technical field of molecular biology, and discloses a saline-alkaline resistant gene MdLAC12 for enhancing apple and application thereof, an extraction method of the saline-alkaline resistant gene MdLAC12 for enhancing apple comprises the following steps: step 1, extracting total RNA (Ribonucleic Acid) from an apple rootstock M9-T337 root system, and taking cDNA (Complementary Deoxyribonucleic Acid) obtained by reverse transcription as a cloning template; 2, designing an MdLAC12 primer according to an apple genome database GDDH13, and carrying out a conventional polymerase chain reaction (PCR); and step 3, carrying out homologous recombination on the obtained PCR product of the MdLAC12 and pMD18-T, transforming a connection product into an escherichia coli DH5 alpha competent cell, and selecting resistant bacterial plaque for sequencing analysis to obtain a CDs sequence of the MdLAC12. The method is helpful for breeding excellent saline-alkaline tolerant apple rootstocks, and can also improve utilization of saline-alkaline land in a prebiotic area. The method has the advantages of simplicity in operation, high saline-alkaline tolerance and low production cost, and can be widely applied to the saline-alkaline tolerance germplasm resource breeding process.

The invention provides a wheat TaPHT1; according to the application of the gene 36 under low-phosphorus stress, through a sequence published in a wheat genome database, a low-phosphorus-resistant spring wheat material SW2 root system total RNA is taken as a template, cDNA is prepared through reverse recording, and TaPHT1 is cloned by taking the cDNA as the template; the method comprises the following steps of: constructing an overexpression vector, carrying out gene function verification on arabidopsis thaliana through transgenosis genetic transformation, and finding transgenosis TaPHT1 compared with wild type arabidopsis thaliana WT; the gene 36 can improve the low-phosphorus resistance, and provides a theoretical basis and gene resources for cultivating low-phosphorus-resistant wheat.

The application discloses a bacterial identification method based on high-throughput sequencing data, comprising the following steps: (1) constructing a high-quality bacterial genome K-mer database and a high-quality bacterial marker gene database; (2) performing quality control on original sequencing data, removing low-quality sequences, adapter sequences and short fragments, and aligning the remaining sequences with a host reference genome to remove host-derived sequences and obtain pure microbial sequences; (3) inputting the pure microbial sequences into Kraken2 software and Metaphlan2 software respectively for independent species annotation to obtain two groups of annotation results; (4) performing cross-validation; (5) taking all retained 'high-confidence species' as final identification results, and calculating relative abundance based on the corresponding Bracken corrected abundance values. The method has important application value in the fields of clinical diagnosis, probiotic health products, pharmaceutical industry and the like.

The invention discloses a crop gene editing optimization method based on an artificial intelligence self-evolution algorithm. The method comprises the following steps: S1, obtaining complete genome data and feature information related to a target gene from a crop genome database; s2, constructing a target model based on the genome data and the feature information related to the target gene, and generating an initial gene editing scheme; s3, creating a genetic memory bank; s4, generating an initial gene editing scheme based on genome data by using a self-evolution algorithm; s5, preferentially reserving the editing scheme with high adaptability to enter the next round of evolution; s6, in each round of iteration, searching a historical editing scheme similar to the current gene editing target from the genetic memory bank, and performing path optimization on a newly generated scheme; s7, triggering a self-adaptive adjustment mechanism to re-optimize editing parameters for the scheme close to the threshold value; and S8, after multiple rounds of evolution are completed, the system outputs an optimized final gene editing scheme. According to the invention, precise generation and dynamic optimization of the gene editing scheme are realized.

The invention relates to the technical field of bioinformatics, in particular to a pathogenic microorganism genome, a construction method, a computer system and application. According to the method, a genome data quality control strategy in the pathogenic microorganism genome database creation process is innovated, ANI and AF double indexes are creatively adopted for classification error recognition, contig pollution sequence recognition and k-mer short sequence pollution recognition are combined for sequence pollution recognition and processing on genome data, the number of genomes is reserved to the maximum, and the number of the genomes is reduced to the maximum. According to the method, contig level sequence errors are accurately recognized, strain specific sequences are prevented from being mistakenly deleted, the diversity of species genomes is guaranteed, and the constructed database can improve the identification accuracy / sensitivity of pathogen infected species.

The invention relates to the technical field of bioinformatics, in particular to a construction method of a dehalogenation microorganism functional genome database and an analysis method of dehalogenation microorganisms. The construction method comprises the following steps: obtaining a dehalogenation reaction related gene; based on a Uniprot protein database, obtaining a seed sequence and a homologous sequence of a family to which a dehalogenation reaction related gene belongs to obtain a core database; comparing the core database with a homologous protein database, and combining the sequence of the dehalogenation functional gene family obtained by comparison with the core database to obtain a preliminary database; and comparing the preliminary database to a Refseq database of microorganisms in NCBI, and carrying out classification, homologous sequence merging and redundancy elimination to obtain a complete database. The accurate dehalogenation function gene database is constructed based on the analysis and search results of a plurality of databases, can be used for conveniently and accurately analyzing the dehalogenation microorganism function community in the environment, and has important application value.

The application discloses application of a rice fertility gene MS2. The application finds a gene MS2 for regulating rice fertility in a rice genome database, the gene is highly expressed during anther development period of rice, nucleotide sequences of the gene are shown in SEQ ID NO. 1, and the amino acid sequences are shown in SEQ ID NO. 2. Research shows that the MS2 gene is related to rice fertility, and influences rice pollen fertility, and knocking out the MS2 gene in wild type rice can make the rice pollen fertility significantly decrease, and the MS2 gene can be applied to creation of a rice sterile line and preparation of hybrid seeds. Meanwhile, the male sterile line generated by mutation of the MS2 gene is not influenced by environmental conditions such as illumination and temperature, the fertility of the male sterile line is stable, a new gene resource is provided for construction of a rice hybrid breeding system, and germplasm resources of the male sterile line are also expanded.

The invention belongs to the field of gene identification, and particularly relates to a method for identifying an invasive plant in a soil environment DNA sample by using chloroplast genome data, which comprises the following steps: constructing an invasive plant chloroplast whole-genome database; collecting samples at a plurality of sample points; eDNA in the sample is extracted; carrying out PCR (Polymerase Chain Reaction) amplification on the extracted eDNA to obtain an amplicon product; sequencing the amplicon product by using a high-throughput sequencing technology to obtain high-throughput data; comparing the intrusive plant chloroplast whole-genome database with the high-throughput data to obtain the species of the intrusive plant species; according to the method, only the extracted eDNA is subjected to chloroplast gene PCR amplification, and exfoliates of animals and microorganisms are screened out, so that the DNA data volume is simplified, and the analysis of invasive plant species in a region can be accurately and comprehensively completed.

The invention provides a method for constructing a clinical-grade respiratory tract pathogenic microorganism detection genome database. Key functions of screening of high-quality genome sequences of species, removal of redundant genome sequences, classification of wrong species of the genome, filtration of pollution sequences in the genome and the like are integrated.

The present application relates to the technical field of bioinformatics, and particularly relates to a construction method of a dehalogenating microorganism functional genome database and an analysis method of dehalogenating microorganisms. The construction method comprises the following steps: obtaining dehalogenation-related genes; obtaining seed sequences and homologous sequences of a family to which the dehalogenation-related genes belong based on a Uniprot protein database to obtain a core database; comparing the core database with a homologous protein database, merging sequences of dehalogenation functional gene families obtained through comparison with the core database to obtain a preliminary database; and comparing the preliminary database to a Refseq database of microorganisms in NCBI, and obtaining a complete database through classification, merging of homologous sequences and de-redundancy. The present application constructs an accurate dehalogenation functional gene database based on analysis and search results of multiple databases, which can be used to conveniently and accurately analyze dehalogenating microorganism functional communities in the environment, and has important application value.

The present invention discloses a genome-based equipment framework application design method, system and device, including: S1, building a genome database; S2, performing gene-performance mapping analysis and gene-environment effect mapping analysis based on the gene database to obtain analysis results and store them in the gene database; S3, performing engineering practice application based on the analysis results. The present invention is based on the equipment genome concept of equipment planning demonstration, engineering development and test identification framework.

The invention relates to a database cleaning method and device, computer equipment and a storage medium. The method comprises the steps that a to-be-cleaned database is obtained, the to-be-cleaned database comprises whole genome sequences of different target species, the whole genome sequences of all the target species are preprocessed, a short sequence fragment set of all the target species is obtained, preprocessing at least comprises splitting and duplicate removal, and a short sequence fragment set of all the target species is obtained; the short sequence fragment set of each target species is compared with a preset gene sequence database of different dimensions to obtain a signal-to-signal comparison result, the gene sequence database at least comprises a target species whole genome database, and a target species whole genome database is obtained based on the signal-to-signal comparison result. And screening out polluted short sequence fragments from the short sequence fragment set of each target species, and carrying out signal generation modification on the whole genome sequence corresponding to the polluted short sequence fragments to obtain a cleaned database. By adopting the method, the reliability of the database can be improved.

The invention provides a potato StTST1 gene and application thereof in cold resistance and drought resistance, through a sequence published in a potato genome database, a total RNA (Ribonucleic Acid) of a leaf of a low-temperature sensitive type Hubei potato No. 3 (E3) is taken as a template, cDNA (Complementary Deoxyribose Nucleic Acid) is prepared through reverse recording, then the cDNA is taken as a template to clone the StTST1 gene, an overexpression vector is constructed, genetic transformation of E3 is carried out for gene function verification, and the potato StTST1 gene is obtained. In combination with an interference strain obtained in the earlier stage, it is found that the interference E3 endogenous StTST1 gene can improve the cold resistance and reduce the drought resistance; the overexpression of the StTST1 gene can improve the drought resistance and reduce the cold resistance.

The invention relates to the technical field of plant genetic engineering, in particular to application of a brassica napus BnPUB12 gene in regulation and control of plant waterlogging tolerance. The BnPUB12 gene is cloned through a sequence published in a brassica napus genome database by taking DNA (Deoxyribose Nucleic Acid) of Zhongdou-11 leaves as a template, a CRISPR / Cas9 gene editing vector targeting the BnPUB12 is successfully constructed and is genetically transformed into the Zhongdou-11 of a brassica napus variety for transgenosis function verification, and an obtained homozygous mutant material is obviously enhanced in waterlogging resistance compared with a wild type material and has a good application prospect. Therefore, the gene can remarkably and negatively regulate the waterlogging stress resistance of the rape. Therefore, the invention provides a new gene resource for adversity stress resistance of rape.