12 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 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 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 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.

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.