23 results about "Gene Annotation" patented technology

The invention provides a full-length gene sequence modeling method and system based on a neural network, and the method comprises the steps: constructing a first expression matrix for initial single-cell RNA sequencing data, and carrying out the quality control transformation of the first expression matrix to obtain a second expression matrix; inputting the second expression matrix into a preset binning embedding module to obtain a binning embedding matrix; maintaining and loading a gene pathway set through a knowledge base and a mapping module to obtain a binary mask matrix, and performing mask processing on the binning embedded matrix based on the binary mask matrix to obtain a pathway mask matrix; the path mask matrix is input into a preset attention state space model, the attention state space model comprises an encoder module, a jump connection module and a decoder module which are arranged in sequence, and a reconstruction tensor is output through the decoder module. According to the scheme, an efficient and extensible whole-gene annotation method is provided, and whole-gene expression input can be processed while the calculation efficiency is kept.

The invention provides a phytophagous insect food web DNA molecular data automatic analysis method and device based on high-pass sequencing and a storage medium, and relates to the field of molecular biological information detection.The method comprises the steps that sequence splicing, screening and species identification are carried out on obtained double-end sequencing data and local and downloaded DNA databases through an automatic system, and a DNA molecular database is obtained; generating an Excel table containing species names and a DNA bar code sequence file; performing comparative analysis on the double-end sequencing data by adopting matching splicing, and generating a contiguous group sequence based on a local DNA database; if the matching splicing cannot generate the effective sequence, generating a new gene file by adopting non-parameter splicing, and performing gene annotation in combination with the downloaded DNA database; all analysis steps are connected in series through standardized parameter input, including gene screening through threshold values and generation of insect recipe identification results. According to the method, the sequencing data can be subjected to full-process automatic analysis through a one-key command, and the efficiency of food web authentication high-throughput sequencing data processing is greatly improved.

The invention belongs to the technical field of bioengineering and microbiomics, and particularly relates to an acquisition method and application of a specific metabolic substrate of lactobacillus crispatus and application of a specific carbohydrate active enzyme CAZzyme gene and a polysaccharide utilization site (PUL). Genomes of lactobacillus crispatus and lactobacillus inertus are obtained from a public database, gene annotation is carried out on the genomes of the lactobacillus crispatus and the lactobacillus inertus, and a random forest model and a KEGG metabolic pathway diagram are combined to find specific CAZzyme genes, PUL and other genes with metabolic functions of the lactobacillus crispatus; a substrate which only lactobacillus crispatus can metabolize is searched based on the genome difference of the two bacteria, and the ability of the obtained substrate for promoting the growth of lactobacillus crispatus and inhibiting the growth of inert lactobacillus is evaluated through experiments. Growth and reproduction of the lactobacillus crispatus are promoted through the substrates, so that the lactobacillus crispatus accounts for a higher proportion in vagina microecology, the vagina is protected, and reproduction of other unfavorable bacteria is reduced. The assisted reproduction success rate is improved.

The present application provides a kind of cytochrome P450 monooxygenase gene and the protein coded by it, recombinant plasmid and application derived from ramie, the coding region sequence of the cytochrome P450 monooxygenase gene derived from ramie is as shown in SEQ ID NO:1, the amino acid sequence of the protein coded by it is as shown in SEQ ID NO:2.The present application takes ramie as research object, obtains ramie cytochrome P450 monooxygenase gene (BnMAX1) by three generations sequencing and gene annotation comparison.Longer coding sequence of the target gene is obtained by PacBio Sequel sequencing, which is simple, fast and easy to operate.The function of the gene is verified by cloning identification, bioinformatics, expression pattern and genetic transformation analysis, which shows that the gene has the effect of relieving plant cadmium toxicity.The acquisition and application of the gene provide basic theoretical support for molecular improvement of cadmium tolerance of ramie, and provide new technical means for how to improve the ecological restoration ability of ramie under heavy metal cadmium stress.

The application discloses a screening method and application of a SNP molecular marker of a PDGF gene related to the number of lambing of a Tianhua mutton sheep flock. F ST The signal is detected, and a molecular marker affecting the number of lambing of the Tianhua mutton sheep flock is screened in combination with gene annotation and site annotation. The molecular marker is located at 3850004 bp of a PDGFD gene of a chromosome 15 of a sheep reference genome (ARS-UI_Ramb_v2.0), and the base mutation is T or C. The molecular marker has a significant influence on the number of lambing of the Tianhua mutton sheep flock, can be applied to the molecular marker for detecting the number of lambing of the Tianhua mutton sheep flock, accelerates the breeding process of the Tianhua mutton sheep, and has the advantages of simple operation, high speed, high sensitivity and the like.

The invention provides a genome annotation method and an electronic device. The genome annotation method comprises the following steps: S1) performing gene structure prediction on a genome by adopting multiple modes to obtain multiple prediction gene sets; s2) performing gene integration on the multiple predictive gene sets by using an EVM tool to obtain an integrated gene set; s3) performing BUSCO evaluation on the integrated gene set to obtain an integrated gene set evaluation file; s4) performing BUSCO evaluation on the genome to obtain a genome evaluation file; and S5) correcting the integrated gene set evaluation file by using the genome evaluation file to obtain a corrected gene set, wherein the gene structure prediction comprises transcriptome prediction, de novo prediction and homologous prediction.The genome annotation method can significantly improve the accuracy and integrity of gene annotation.

This invention, belonging to the field of bioinformatics, discloses a cross-species prediction method for peptide-encoding sequence-dependent open-type recurrent (sORF) proteins. The method integrates protein-encoding DNA sequences from human and mouse sORF databases, Arabidopsis thaliana from the TAIR database, and some prokaryotes from the NCBI database. Positive and negative samples corresponding to each species are constructed using data filtering and negative sample generation strategies. Sequence features are extracted and the training set is screened using maximum relevance minimum redundancy and incremental selection methods to obtain the optimal feature sets corresponding to different methods and construct a peptide-encoding sORF prediction model. Parameters are optimized using a greedy grid search method to construct the optimal prediction model based on a support vector machine. The prediction model is evaluated using sensitivity, specificity, accuracy, and the Matthews correlation coefficient. This method facilitates the classification and identification of peptide-encoding sORFs and is of great significance for the study of peptide-encoding sORFs and gene annotation.

This invention provides a gene prediction and identification method, apparatus, device, and storage medium, belonging to the field of gene annotation and prediction. The method includes: acquiring the gene text to be annotated and a set of promoter-terminator pairs; preprocessing the gene text to generate a raw genome sequence; searching the raw genome sequence for base sequences that fuzzy search matches the set of promoter-terminator pairs to generate a base sequence to be aligned; and comparing the base sequence to be aligned with base sequences in a bioinformatics database based on the BLAST gene alignment method to generate gene prediction and identification results. This invention, by separating base sequences from promoter-terminator pairs and then performing BLAST gene sequence alignment, achieves coarse gene localization followed by BLAST gene sequence alignment, providing a method for predicting new genes, improving alignment efficiency and comprehensiveness, as well as the accuracy and comprehensiveness of gene prediction results.

This invention discloses a method for microbial association gene mining that combines whole-genome sequencing and metagenomic sequencing, specifically relating to the field of bioinformatics data processing technology. The method includes acquiring host whole-genome sequencing data, metagenomic sequencing data, and sample attribute data of a target population. Within an industrial cloud computing environment, it performs biallelic locus extraction, genotype quality control, calculation of the relative abundance of the target microorganism, and resolution of fixed terms and principal component terms, outputting a locus table, abundance table, fixed term table, and principal component term table. By performing inclusion and removal comparisons on each fixed term and principal component term, the method resolves the association differences of the same host locus under different covariate compositions, determines the dominant terms accordingly, and then combines gene annotation to screen out conditionally dominant loci and candidate genes.

The present application relates to the technical field of plant gene function, and aims to provide a construction method of a homologous silencing system of a Paeonia lactiflora bud dormancy gene, comprising the following steps: designing amplification primers according to gene annotation and a conserved sequence region in a Paeonia lactiflora bud dormancy full-length transcriptome, and constructing a conserved sequence fragment of a target gene into Agrobacterium tumefaciens containing a pTRV vector; taking a rhizome of a treated Paeonia lactiflora annual seedling as an infection material, and placing the infection material in Agrobacterium tumefaciens liquid containing pTRV1, pTRV2 and pTRV2-target gene fragments to perform infection treatment; potting the rhizome and moving the rhizome into a culture room to perform culture, observing phenotype and expression amount differences between the rhizome and a control group in a growth process, and confirming that the homologous silencing system is successfully constructed. The present application first completes miniaturization treatment and batch bacterial liquid infection of an underground rhizome system of Paeonia lactiflora, establishes a virus-mediated homologous function silencing system of a Paeonia lactiflora bud dormancy gene, and realizes the purpose of verifying functions of bud dormancy and even germination and growth related genes.

The invention relates to a method for rapidly carrying out BSA (Bovine Serum Albumin) gene localization by utilizing a space mutation mutant. The method comprises the following steps: firstly, carrying propagules such as seeds through an aerospace craft, and constructing a broad-spectrum mutant library by utilizing space environment mutagenesis; returning to the ground, culturing and screening M1-generation mutants with target excellent characters, and hybridizing / backcrossing with a wild type to construct a character segregation population; by adopting a group separation analysis (BSA) strategy, selecting phenotype polar differentiation individuals, and respectively mixing the phenotype polar differentiation individuals to form a high-value pool and a low-value pool; and finally, carrying out whole genome high-throughput sequencing on the double pools and the parents, rapidly locking a genome region linked with a target character by combining bioinformatics analysis such as SNP-index and the like, and verifying candidate genes through gene annotation, molecular marking and gene editing. According to the invention, the broad spectrum of space mutagenesis and the high efficiency of the BSA-seq technology are integrated, the period from mutation creation to gene identification is remarkably shortened, and an innovative technical scheme is provided for crop genetic improvement and functional genomics research.

The invention relates to a DNA (Deoxyribose Nucleic Acid) of a gene OsMKKK32 for regulating and controlling rice grain shape, thousand grain weight and salt tolerance and breeding utilization of a protein of the gene OsMKKK32. The grain width major gene OsMKKK32 is cloned by performing QTL (quantitative trait loci) analysis on the grain width character of an RIL group constructed by backcrossing the GXB (GXB) and the Dular for many years and combining quantitative analysis and gene annotation. By adopting a gene editing and molecular marker assisted breeding technology, an OsMKKK32 knockout near-isogenic line material and a near-isogenic line material with different haplotypes are obtained. The OsMKKK32 is knocked out or the expression of the OsMKKK32 is reduced, so that the grain width, the grain thickness and the thousand grain weight of rice grains are remarkably reduced, and the grain length is remarkably increased. Salt tolerance analysis shows that the expression of the OsMKKK32 gene is inhibited by salt, and the salt tolerance of the rice is remarkably improved by knocking out the OsMKKK32. The OsMKKK32 different haplotype near-isogenic line material provides material and technical support for high yield of rice and cultivation of saline-alkaline tolerant rice.

A species feature descriptor construction method based on functional genomics is beneficial to providing a new method for toxicity prediction and risk assessment modeling of chemicals to multiple species, and is characterized by comprising the following steps: step 1, collecting proteome data of a target species; 2, deploying a software tool for extracting the functional gene information of the species on a cloud server, and developing a command line tool for the software tool to realize gene annotation of multiple species and uploading and downloading of data; 3, importing the proteome data into the tool software for query, matching and annotation to obtain functional genome information of the target species; step 4, preprocessing and visualizing the annotated functional genome information; and step 5, constructing species feature descriptors of multiple species based on the functional genome information.

The invention provides a ramie-derived cytochrome P450 monooxygenase gene, a protein coded by the ramie-derived cytochrome P450 monooxygenase gene, a recombinant plasmid and application of the ramie-derived cytochrome P450 monooxygenase gene, the sequence of a coding region of the ramie-derived cytochrome P450 monooxygenase gene is shown as SEQ ID NO: 1, and the amino acid sequence of the protein coded by the ramie-derived cytochrome P450 monooxygenase gene is shown as SEQ ID NO: 2. According to the invention, ramie is taken as a research object, and the ramie cytochrome P450 monooxygenase gene (BnMAX1) is obtained through three-generation sequencing and gene annotation comparison. A longer coding sequence of a target gene is obtained through PacBio Sequel sequencing, and the method is simple, rapid and high in operability. The gene is subjected to cloning identification, bioinformatics, expression pattern and genetic transformation analysis and the like to verify the function of the gene, which indicates that the gene has the effect of relieving plant cadmium toxicity. The acquisition and application of the gene provide basic theoretical support for molecular improvement of cadmium tolerance of ramie, and provide a new technical means for improving ecological restoration ability of ramie under the stress of heavy metal cadmium.

The invention relates to the technical field of molecular biology and genetic breeding, in particular to a peanut pod cracking force site, a molecular marking method and application. The method comprises the following steps: S1, performing phenotype identification and QTL (Quantitative Trait Locus) analysis, and performing QTL scanning through ICIMapping V4.2 software in combination with an existing genetic map and population genotype information; s2, acquiring an SNP site and developing a marker, and discovering that A / G single nucleotide polymorphism variation exists at the 139316601 position of the B04 chromosome of the VX7G96 gene and causes termination mutation through analysis of gene annotation information in an interval and analysis of sequence difference between parents; and S3, verifying the molecular marker B04-139316601F and the molecular marker B04-139316601R which are linked with the pod splitting character, and carrying out qPD. B04 site detection on a strain of a recombinant inbred line group by utilizing the molecular marker B04-139316601F or the molecular marker B04-139316601R. The peanut pod cracking force site qPD.B04 and the molecular marking method provided by the invention have remarkable technical advantages. 10.17%-13.61% of the qPD.B04 locus showing variation can be explained through accurate positioning, and close association between key candidate genes and pod cracking characters is determined by combining functional analysis of the homologous gene VX7G96 of arabidopsis SEP2.

The application discloses a kind of based on rice infected tissue transcriptome sequencing of SRBSDV Quantitative method of virus, comprising: 1) obtain the genome assembly and gene annotation file of SRBSDV virus, and the high-throughput transcriptome sequencing original data of rice virus infected tissue;2) construct SRBSDV virus genome index module;3) obtain the non-redundant length of each gene in SRBSDV virus genome annotation file;4) obtain high-quality transcriptome sequencing data;5) obtain the total number of short reads of each sample in step 4);6) obtain individual level BAM file;7) obtain the original expression of different genes in each sample Virus;8) obtain gene expression standardization function FPKB.The application can more accurately evaluate the infection level of virus by means of standardized bioinformatics analysis framework;And more virology information can be mined, the maximization of data utilization is realized, support is provided for virus research and prevention and control, and the accuracy of virus quantification is improved.

The application discloses a dikaryon inter-nuclear allelic expression analysis method and device and a storage medium, relates to the field of bioinformatics transcriptome analysis of dikaryophyte fungi, and the method comprises the following steps: performing alignment analysis on sequencing data of dikaryophyte fungi and two nuclear reference genomes respectively; performing nuclear source classification on each read in the sequencing data by using an SVM model; taking all gene sequences of nucleus 1 as a query set, taking gene sequences of nucleus 2 as a target set, and using a BLAST tool to construct a similarity score matrix between the gene sequences; combining the similarity score with gene annotation information, analyzing and establishing an inter-nuclear allelic relationship by using a LightGBM model; generating a counts file, performing FPKM standardization processing, combining the expression after the standardization with an inter-nuclear allelic relationship index for analysis, and obtaining an analysis result. Through the application, inter-nuclear allelic analysis of dikaryophyte fungi is realized.

The invention belongs to the field of bioinformatics and genomics, and discloses a method for rapidly and accurately predicting an intron splicing site of a target species. The method comprises the following steps: 1) obtaining a genome sequence and transcriptome sequencing data of a target species; 2) screening annotation genes and constructing a training set and a test set; 3) performing learning training on splicing site information by adopting a deep learning model architecture combining a convolutional neural network, a bidirectional long-short-term memory network and a self-attention structure; 4) performing bit-by-bit prediction on the input gene sequence by using the model obtained by training; and 5) judging the position of the splicing site according to the prediction score, and labeling and re-evaluating the abnormal or low-credibility splicing site. The calculation model provided by the invention can learn key sequence features at splicing sites, and can be extended to various species through transfer learning to realize high-precision introne boundary prediction. According to the method, the gene annotation efficiency can be remarkably improved, splicing abnormity caused by mutation can be accurately recognized, and the method has important application value for genomics research and gene function analysis and regulation.

A system includes an aquaculture system, a plankton treatment system, a gene expression database, a plankton analysis system, and an output module. The plankton processing system collects and processes a plankton sample, extracts and sequences RNA, and performs a bioinformatics analysis including gene annotation, transcriptome assembly, and gene expression quantification, thereby outputting gene expression data to the gene expression database. The plankton analysis system retrieves and analyzes gene expression patterns to assess plankton states and ecological effects. The plankton analysis system includes an AI-based module that establishes a correlation between gene expression and ecosystem conditions, and a rule-based module that analyzes gene function using predefined biological rules. The output module generates a report that provides insights to plankton health, nutrient circulation, and aquaculture ecosystem conditions.

The invention discloses a computer device and method for detecting target phenotype related genes or candidate genes based on low-depth sequencing data and application. The present invention uses a 29-mer sequence representing each SSP gene at the generic genome level to reveal gene diversity that has not been explored between different wheat varieties and modern cultivated varieties. The SSP gene related to the processing quality is identified based on the whole genome association study of k-mer so as to improve the wheat processing quality. The device or the method provided by the invention can be applied to screening, mining and cloning of phenotypic character related candidate genes with insufficient gene annotation caused by numerous coding genes, complex structures, existence of a large number of long and short repetitive sequences in the genes and existence of a large number of non-communicated regions in coding sequences and flanking sequences; and annotation of related gene functions, correlation analysis and molecular marker development are carried out.

The application discloses a real-time fluorescent quantitative PCR internal reference gene of Onychostoma rhabarbarium and a screening method and application thereof. The application is based on Onychostoma rhabarbarium genome assembly and gene annotation work, and 18 candidate internal reference genes are screened according to transcriptome data of 10 different tissues. The expression of the 18 candidate internal reference genes in different tissues of the Onychostoma rhabarbarium and the stability of the expression in different tissues are detected by a qPCR method, and the result shows that, tubb4b , eif2s2 , eif3a or rps27l the expression is most stable in various tissues, and the combination of the internal reference genes is recommended as the internal reference gene group of the qPCR experiment of the Onychostoma rhabarbarium. The result of the application lays a foundation for functional gene research of the Onychostoma rhabarbarium, especially expression mode research of the functional gene in various tissues, and provides a molecular biology basis for resource protection and artificial breeding of the Onychostoma rhabarbarium.

A system includes an aquaculture system, a plankton processing system, a gene expression database, a plankton analysis system, and an output module. The plankton processing system collects and processes plankton samples, extracts and sequences RNA, and performs bioinformatic analysis, including gene annotation, transcriptome assembly, and gene expression quantification, outputting gene expression data to the gene expression database. The plankton analysis system retrieves and analyzes gene expression patterns to assess plankton status and ecological roles. The plankton analysis system includes an AI-based module, which establishes correlations between gene expression and ecosystem conditions, and a rule-based module, which analyzes gene functions using predefined biological rules. The output module generates a report providing insights into plankton health, nutrient cycling, and aquaculture ecosystem conditions.

The present invention relates to the field of gene sequencing technology, and discloses a method for assessing the pathogenicity of mutant genes based on a Bayesian algorithm, comprising: comparing high-throughput sequencing data with human genome sequences to obtain gene mutation data, annotating gene mutation sites to obtain a high-throughput sequencing annotation table, extracting evidence description features from the high-throughput sequencing annotation table according to the evidence source category, extracting evidence weight levels according to the evidence source category and the evidence description features, obtaining an evidence weight level set, calculating the pathogenicity posterior probability of the gene mutation site using the evidence weight level set, and querying the pathogenicity assessment level in the gene pathogenicity assessment table using the pathogenicity posterior probability. The present invention also proposes a mutant gene pathogenicity assessment device, electronic device, and computer-readable storage medium based on a Bayesian algorithm. The present invention can solve the problems of low accuracy and high labor consumption in the current assessment of the harmfulness of mutant genes.