59 results about "Gene Annotation" patented technology

The invention relates to a CRISPR-Cas9 system sgRNA action target screening method. The method comprises the steps of (1) obtaining segments with 5'-Nx-NGG-3' sequences (x is an integer ranging from 19 to 22 and N represents A/T/C/G) in genomes by utilizing whole genome sequences and gene annotation information of published species to serve as candidate targets of CRISPR-Cas9 system sgRNA; (2) fragmenting the genomes into fragments of 22-25bp and screening sequences ending with NGG and non-repeated on the genomes; and (3) comparing the sequences of the candidate targets in the step (1) with the screened sequences in the step (2), and performing screening and sorting on corresponding optimal sequences according to mismatch information and a selection formula to obtain an optimal genome sgRNA action target set. The invention furthermore provides an apparatus used for realizing the screening method. The method is suitable for all species with known genomes and gene annotation information, and a universal sgRNA sequence set of whole genome level of the species is quickly and efficiently obtained to build a gene knockout mutant library or a gene knockout animal model.

The present invention provides systems and methods for analyzing gene expression, gene annotation, and sample information in a relational format supporting efficient exploration and analysis, including comparative differential expression analysis, expression pattern matching, and mapping of external attributes or identifiers to internal representations of gene fragments or samples.

The invention discloses a gene analysis annotation method and device. The method comprises the following steps that: capturing first gene data from at least one existing gene database; storing the first gene data in a uniform format, and constructing an annotation gene database; obtaining a standard file used for describing genome variation, and extracting a retrieval value from the standard file; according to the retrieval value, carrying out retrieval in the annotation gene database to obtain second gene data, wherein the retrieval value comprises the chromosome number of a variation site, the starting position of the variation site, the basic group of a refereed genome and the basic group of the variation site; and according to the second gene data, carrying out gene annotation on the standard file, and generating a gene analysis annotation result report. By use of the method, the gene analysis annotation can be accurately and efficiently carried out.

The invention discloses a method for detecting a variable spliceosome in a third generation full-length transcriptome. The method comprises the following steps: merging original annular test sequences with joints removed to form a monomolecular transcript sequence, and screening a third generation full-length transcript sequence; comparing the third generation full-length transcript sequence with a reference genome sequence, and screening a third generation full-length transcript sequence having coverage and similarity with the reference genome sequence larger than preset thresholds; carrying out splicing false positive filtration and DNA contamination filtration on the screened third generation full-length transcript sequence; and carrying out gene annotation and variable spliceosome annotation on the filtered third generation full-length transcript sequence. An overlong read length of a third generation sequencing technology mentioned in the method disclosed by the invention is large enough to cover most RNA, the third generation full-length transcript sequence can be obtained by SMRT sequencing transcriptomes without being assembled, and a splicing structure of a gene can be effectively obtained by third generation transcriptome sequencing, and more perfect gene model annotation can be constructed.

The invention discloses a metagenome data analysis method based on a next-generation sequencing technology, which comprises the following steps of: (1) carrying out quality control on original sequencing data to obtain clean reads; (2) performing species annotation on the clean reads subjected to the quality control; (3) performing statistical analysis on the sample diversity based on a species abundance matrix; (4) performing statistical analysis on species with significant differences among sample groups based on the species abundance matrix; (5) splicing and assembling the clean reads to obtain a contigs sequence; (6) packaging the contigs obtained by splicing and assembling into boxes to obtain bins; (7) carrying out gene annotation on the bins subjected to boxing; (8) performing statistical analysis on the genes with significant differences among the sample groups based on the gene abundance matrix; and (9) based on the gene annotation result, performing function and species annotation on the sequence. A whole process from metagenome next-generation sequencing data processing to species composition analysis, gene composition analysis and function annotation is provided, an accurate analysis result is provided for researchers, and the metagenomics problem is comprehensively analyzed.

The invention relates to a method for detecting chromosome microdeletion and micro-duplication of a human embryo. The method comprises the following steps of performing whole genome amplification on cells cultured in vitro, interrupting DNA (deoxyribonucleic acid) molecules, and sequencing DNA fragments to obtain sequencing reads; comparing the sequencing reads with a reference sequence, and positioning the sequencing reads on the reference sequence; screening non-repeated areas of the reference sequence, and reserving the non-repeated areas; establishing a matrix of read number in windows through normal samples, analyzing the data of the normal samples, performing statistics on the read number of all the windows in the non-repeated areas, and establishing a probability matrix of the read number and chromosome enpeoids; calculating the copy number, i.e., the A/B/C state, of loci; selecting m continuous loci, i.e., the A state, as micro-duplication loci, and selecting m continuous loci, i.e., the C state, as microdeletion loci; contrasting the micro-duplication loci and the microdeletion loci with the existing CNV (copy number variation) and disease database, performing basic gene annotation and gene function analysis which relates to deletion parts, and annotating with a microdeletion syndrome disease type.

The invention discloses a novel cucumber SNP molecular marker. The mark number of the novel cucumber SNP molecular marker is SLAF7695. According to the novel cucumber SNP molecular marker, the simplified genome depth sequencing technology is utilized, 73100 SLAF labels are obtained totally, 5355 polymorphic markers of three types including SNP, EPSNP and INDEL are obtained through polymorphic analysis, and 140 different markers closely related to cucumber powdery mildew resistance are obtained and mainly concentrated on the first chromosome and the sixth chromosome. Two candidate areas related to powdery mildew resistance characters are successfully located, seven special markers closely linked with cucumber powdery mildew resistance are obtained, 28 genes and related annotation information are obtained through gene annotation, and five genes are related to the functions of defense response, harm response, toxin catabolism, cell stress response and the like. The novel cucumber SNP molecular marker provides a theoretical foundation for exploration of cucumber powdery mildew resisting mechanism and molecular marker assisted selective breeding.

The invention belongs to the technical field of aquatic breeding, and particularly relates to a growth-related molecular marker in a C-type scavenger receptor gene (LvSRC) of Litopenaeusvannamei and application thereof to genetic breeding of the Litopenaeusvannamei. A batch of markers related to shrimp growth traits are positioned in the genomic level through genome-wide association analysis, a single nucleotide polymorphism (SNP) marker (LvSRC-211-G/T) positioned in a coding region of the LvSRC gene is further screened through gene annotation and by a candidate gene association analysis method, and the genotype of the marker is significantly correlated to the shrimp growth traits (P is smaller than 10<-6>). The marker is positioned at a 211bp position on the LvSRC gene and belongs to G/Ttype mutation, and the GT genotype of the marker is a distinct growth-dominant genotype. The marker provided by the invention can be used as the shrimp breeding molecular marker for assisting in genetic selection of the shrimp growth traits.

The invention relates to a health data analysis report generating system and method based on gene sequence analysis. The system comprises a diseases database module, a manual annotation module, a dataacquisition module, a data analysis module, a data storage module, a template library and a report generation module, wherein the data acquisition module, the data analysis module, the data storage module, the template library and the report generation module are sequentially connected, the diseases database module is connected with the template library, and the manual annotation module is connected with report generation module. According to the system, a health analysis report is generated by the aid of a mode combining an automatic retrieval diseases database with a manual annotation supplementary information, contents are automatically, conveniently and rapidly searched by a computer, labor is saved, a health analysis report generating link is simplified, Chinese version of gene annotation databases is absent at present, a computer system cannot automatically capture data, the contents of the report can be more all-round by the aid of manual annotation, understanding of readers isfacilitated, and practical application requirements are met.

The invention belongs to the field of gene annotation and in particular relates to a method for predicting RNA coding potential. The method (named as CPPred) comprises the following steps: by integrating multiple sequence characteristics, particularly describing global distribution of RNA by using CTD; taking redundancy and relevance among candidate characteristics as standards, and combining a characteristic increasing selection method to select an optimum characteristic set to serve as a characteristic vector; establishing a prediction model by a support vector machine (SVM); finally, acquiring the prediction result according to a to-be-predicted RNA sequence characteristic vector. The prediction method provided by the invention is equivalent to a current existing method (having accuracyreaching 90% or higher) while predicting a long RNA sequence, while the method is obviously better than the current existing method while predicting a short RNA sequence.

The application discloses a virus integrated DNA enrichment method, a sequencing data analyzing method and a device. The enrichment method of the application comprises the steps of primer hybridizing and extending, magnetic bead separating and washing. The sequencing data analyzing method disclosed by the application comprises the steps of data filtering, splicing and assembling, comparing and breakpoint judging and gene noting. According to the enrichment method disclosed by the application, specific primers are adopted for extending virus genome target genes so as to replace a long probe, so that the cost is low, the efficiency is high, the specificity is high, and the enrichment time is shortened. Compared with a complete genome, the sequencing data analyzing method disclosed by the application can save data amount, can obtain higher sequencing depth, can obtain more virus DNA breakpoint information and integration position information on the host genome, and can obtain clonal integration events supported by more reads, and besides, can detect non-clonal integration supported by single reads, so as to construct a comprehensive prospect integrated on the host genome.

The invention relates to a method for detecting RNA level gene fusion, electronic equipment and a computer storage medium. The method comprises the following steps: receiving whole genome comparison information and whole transcriptome comparison information; clustering the paired maladjusted read lengths to generate a plurality of large clusters; carrying out whole-genome-level gene annotation onthe large clusters meeting a first preset condition so as to generate first gene combination names for identifying the large clusters based on the corresponding genes; based on the whole transcriptomecomparison information, performing whole transcriptome-level gene annotation on the plurality of paired read lengths so as to generate a second gene combination name for identifying the plurality ofpaired read lengths based on the corresponding gene; and identifying the same corresponding genes associated with the first gene combination name and the second gene combination name so as to determine the same corresponding genes as potential fusion genes. The method is beneficial to rapid and correct recognition of false positive results, and the false positive results of a gene fusion detectionresult can be obviously reduced.

The invention discloses a construction method and system of a microbial gene database, and belongs to the technical field of gene database construction. The method comprises the following steps: acquiring target microbial genome data, and performing gene prediction on the acquired genome data to obtain a gene annotation file containing sequence and species annotations; obtaining a representative gene of each target microorganism; respectively comparing each gene in the representative genes to a nucleic acid sequence database to obtain a comparison result; and filtering a comparison result to obtain gene annotation species information, and reserving genes of annotation species which are the same as the source species, so as to construct the microbial gene database. The microorganism gene database constructed by the construction method can be updated according to the change of the target microorganism, the real-time performance is higher, and the microorganism database constructed by the method only contains the gene sequence of the target microorganism, so that the comparison time is shorter.

The invention belongs to the technical field of bioinformatics, and relates to a method for identifying esophageal squamous cell carcinoma markers on the basis of network index difference analysis. The method comprises the following steps of processing esophageal squamous cell carcinoma gene sample data and normal gene sample data to construct an esophageal squamous cell carcinoma gene interactionnetwork and a normal gene interaction network; using a network module identification method to find out key community structures in the two networks, and performing gene function enrichment analysison the key community structures; extracting same nodes from the two networks, and retaining nodes linked to the same nodes to obtain the two simplified networks; using a global index and a local modular index, analyzing the two simplified networks to obtain genes related to esophageal squamous cell carcinoma; combining a gene function enrichment analysis result with gene annotations and functionalreferences to finally determine candidate markers for diagnosis of esophageal squamous cell carcinoma. A method for studying the esophageal squamous cell carcinoma markers on the basis of gene network difference analysis is further perfected.

The invention discloses an antibiotic drug resistance gene influence factor and difference analysis method. The method comprises the following steps: inputting sample metagenome data and phenotype information of a corresponding sample; annotating the antibiotic drug-resistant gene to obtain an antibiotic drug-resistant gene abundance file; performing antibiotic drug resistance gene influence factor analysis: performing PERMANOVA analysis to obtain a phenotype which has obvious influence on the antibiotic drug resistance gene; carrying out antibiotic drug resistance gene difference analysis: carrying out two-group mean value comparison by utilizing Wilcoxon test and FDR correction, and carrying out more than two-group mean value comparison by utilizing Kruscal-Wallis test, multiple comparison in a PMCMR packet and FDR correction; and judging the change trend of the content of the antibiotic resistance gene. The antibiotic reference database is better adapted to increase of antibiotic resistance sequences, and the multi-module combinatorial analysis method enables analysis of antibiotic resistance genes to be more comprehensive and systematic; and meanwhile, a data set splitting and recombining method is used for obtaining an intersection of multi-data-set analysis results, so that the reliability of the results is improved.

The invention discloses a method for analyzing phylogenetic development of babylonia formosae based on complete mitochondrial genomes, and relates to the field of analysis of the phylogenetic development of the babylonia formosae. The method for analyzing phylogenetic development of the babylonia formosae based on the complete mitochondrial genomes comprises the following steps: 1) sample collection: collecting babylonia formosae extracting mitochondrial genomes DNA; 2), disrupting and purifying the mitochondrial genomes DNA and then building a DNA sequencing library; 3), obtaining a DNA cluster; 4), sequencing the babylonia formosae mitochondrial genomes DNA; 5), comparing the babylonia formosae mitochondrial genomes with other babylonias having known sequences, and then noting encoded protein genes; and 6), comparing a nucleotide sequence of each gene of the babylonia formosae extracting mitochondrial genomes DNA and an amino acid sequence deduced by the nucleotide sequence with other caenogastropoda species, and performing series connection and then analyzing the phylogenetic development. According to the phylogenetic analysis method of the babylonia formosae based on the complete mitochondrial genomes disclosed by the invention, based on the complete mitochondrial genomes, the phylogenetic development of the babylonia formosae is analyzed, complete data of the complete mitochondrial genomes of the babylonia formosae are obtained, and thus, phylogenetic development is performed, and analysis is performed conveniently and effectively.

The cell-based assays described in the present invention can be used to directly assess the sensitivity and specificity of the gene annotation reagent against its target, and to determine if a non-targeted gene participates in a pathway of interest or is functionally linked to another gene or protein. The combination of annotation reagents with such cell-based assays is useful for mapping genes (proteins) into cellular pathways on a genome-wide scale. Preferred assay embodiments include fluorescence or luminescence assays in intact (live or fixed) cells. Such fluorescence or luminescence assays include high-throughput or high-content assays for protein activity, subcellular localization, post-translational modifications, or interactions of proteins. Suitable assays may include protein-protein interaction assays; protein translocation assays; and post-translational modification assays. The invention can be used to assess the efficacy of any gene silencing experiment, to determine the level of gene silencing that is achieved, and to map novel genes into biochemical pathways, and to identify novel pharmaceutical targets. The results also demonstrate the feasibility of employing this strategy in genome-wide functional annotation efforts.

The invention discloses a development method of a strawberry functional gene linked SSR marker. The development method comprises the following steps: (1) acquiring strawberry genome public data; (2) performing quality control processing on the data, assembling and splicing the processed sequences, and identifying a microsatellite sequence; (3) designing primers on a flanking sequence of the microsatellite sequence; (4) performing transcriptome sequencing, splicing and gene annotation of different strawberry varieties; and (5) carrying out electronic PCR anchoring on primers to specific genes.The SSR marker of the method has the advantages of high polymorphism, good codominance, good repeatability and the like. 2468 SSR markers and primers thereof are provided for strawberries, and the markers are all related to functional genes, so that a favorable tool is provided for strawberry breeding and gene mining related to agricultural traits.

The invention is applicable to the technical field of medical genetics, and provides a novel method for quickly annotating genes and mutations by constructing an information query database with complete annotations. The method comprises the following steps: (1) simulating to generate three potential mononucleotide variations of each base site of a human genome, and integrating the variations of different populations in a plurality of common databases to construct a database including all possible gene variations of the human genome; (2) further integrating common genome annotation informationon the basis, and establishing a genome annotation library including all variation information and annotation information of human beings into a whole and more than 9 billion pieces of information; and (3) quickly completing information extraction, pathogenicity prediction, visualization and other content in a query mode according to the database. According to the method, a complex gene annotationprocess is changed into a one-stop query process, so that the problems of non-uniform formats, complicated operation and low efficiency caused by matching different gene variations in multiple databases one by one are avoided.

The invention provides a method and a system for quickly comparing whole genome annotation intervals. The method comprises the following steps: S1, respectively obtaining a gene annotation interval A fragment coordinate set and a gene annotation interval B fragment coordinate set; s2, combining the coordinates of the fragment set A and the coordinates of the fragment set B to obtain a combined fragment set; s3, performing redundancy elimination operation and sorting operation on the combined fragment set; s4, calling a preset interval intersection function to calculate the intersection of all the annotation intervals in the merged fragment set in a single cycle; and S5, outputting a calculation result of the preset interval intersection function. According to the method, the intersection of different types of gene annotation intervals can be rapidly calculated, and compared with a traditional comparison method, the method is simple in implementation logic, small in calculation amount, accurate in judgment and beneficial to improvement of comparison efficiency.