37 results about "Genome alignment" patented technology

The invention discloses a genomic-data storage method. The genomic-data storage method includes the steps that in the genome comparison process, gene-sequence comparison information is obtained, and gene-sequence statistical information is established; the gene-sequence comparison information is stored in a magnetic disk, and according to comparison positions of the gene-sequence comparison information in a genome, corresponding indexes are stored in a memory, wherein the indexes are storage positions of the gene-sequence comparison information in the magnetic disk; genome statistical information is classified, and first statistical information and second statistical information are obtained; the first statistical information is stored in the memory, wherein the first statistical information is statistical information with the access frequency higher than the preset frequency in the variation detection process; the second statistical information is stored in the magnetic disk, wherein the second statistical information is statistical information which cannot be stored in the memory and / or statistical information with the access frequency lower than the preset frequency in the variation detection process. The invention also discloses an electronic device with the genomic-data storage method.

The invention discloses a two step genome comparison method for designing a quantitative PCR specific primer of guizhouense NJAU 4742. At first, full genome sequence of NJAU 4742 is compared in NCBI database and JGI database; genome segments, which are not matched and greater than 500 bp, are picked out; then the screened segments are compared with the full genome of a guizhouense strain 916; anda primer sequence with unique bases is designed. At the same time, three pairs of primers, which are prepared by inserting labeled segments into a gfp labeled strain (gfp-NJAU 4742), are used to examine the specificity of the primers designed based on the genome. By examining the amplification specificity of strains of same genus and different species, re-detecting the soil addition, and actuallydetecting the potting soil, an optimal quantitative PCR primer is screened out. The provided primer design method and design strain specific primer can be applied to quantitative PCR specific primer design of other strains and quantifying of guizhouense NJAU 4742.

The invention discloses a method for data analysis of miRNA in animals with reference data based on a miRBase database. The method is characterized by comprising the following steps of preparation, filtration of logout data, genome alignment, small RNA annotation, miRNA feature analysis, miRNA expression quantity analysis, miRNA function and pathway analyses, and result sorting. The method disclosed by the invention has the beneficial effects that an analysis result is complete, and comprises involved miRNA analysis content and other detected small RNA information annotation, automated analysis is achieved, and statistics and sorting of all analysis content and results can be automatically and rapidly conducted only by providing related database information. All operation steps are visible, and thus errors can be conveniently checked, applied command lines and parameters and log results generated in operation can all be recorded when analysis is conducted step by step, and once a program fails during running, the errors can be rapidly queried.

The invention provides an excavation method for a salt-tolerant gene of salix matsudana. The method comprises the steps that salt-tolerant salix matsudana and salt-sensitive salix matsudana are crossbred to obtain an F1 population, the F1 population is divided into salt-tolerant and salt-sensitive filial generations, and through salt stress, root systems of the salt-tolerant and salt-sensitive filial generations are subjected to transcriptome sequencing to obtain differential expression gene sequences separately; based on the salt-tolerant filial generation, a high-density genetic map is established, salt tolerance QTLs positioning is conducted, a QTL section is obtained through calculation, the QTL section, the differential expression gene sequences and a salix matsudana whole genome arecompared, and through analysis, the salt-tolerant candidate gene is obtained; through salt stress, the relative expression of the salt-tolerant candidate gene of the salt-tolerant filial generation ismeasured, the salt-tolerant candidate gene is determined as a salt-tolerant re-selection gene, instantaneous conversion is conducted, a salt-tolerant physiological index of a salix matsudana seedlingis detected, and the salt-tolerant re-selection gene is determined as a salt-tolerant gene. According to the excavation method, the problem is solved that during traditional salt-tolerant salix matsudana breeding, the salt-tolerant gene cannot be accurately found out.

A method (100) for analyzing a target genome, comprising: (i) aligning (120) sequencing data from the target genome to a reference genome; (ii) identifying (130) heterozygous locations, comprising an identification of allele variants and a frequency of each allele, the allele variants comprising both a reference allele variant and a non-reference allele variant; (iii) generating (140) an alternate reference genome, wherein the identified non-reference allele variant for the identified heterozygous locations replaces the reference allele variant in the reference genome; (iv) aligning (150) sequencing data to the alternate reference genome; (v) identifying (160) a frequency of the allele variants at each of the heterozygous locations; (vi) assessing (170) alignment bias at the identified heterozygous locations, comprising comparing the frequency of allele variants from the reference genome alignment to the frequency of allele variants from the alternate genome alignment; and (vii) generating (190) a report comprising the assessment of alignment bias.

The invention provides an assembling method and an assembling device for a chromosome level genome. The assembling method comprises the following steps: acquiring a known chromosome level genome of the same species as a reference genome; comparing the contigs or scaffolds of the individuals to be assembled with the reference genome to obtain corresponding coordinate information; and according to the coordinate information, mounting the contigs or scaffolds of the to-be-assembled individuals to chromosome levels to obtain chromosome level genomes of the to-be-assembled individuals. For a species which is difficult to provide Hi-C data, the published chromosome level genome of the same species is used as a reference genome, and a contig or a scaffold level genome of a newly detected individual is compared to the reference genome, so that the aim of mounting the newly detected individual to a chromosome level with parameters is fulfilled.

The invention relates to a detection method for whole genome copy number variation (CNV). The method comprises the following steps: (1) obtaining a sequencing result sequence of whole genome sequencing of a DNA sample; (2) comparing the sequencing result sequence with a human reference genome, and calculating the coordinate position of the CNV in a chromosome section and the copy number CN<detection> of the CNV in the section; and (3) calculating the comprehensive CNV<score> of the DNA sample through corresponding formula in which the CNV<length> represents the length of the CNV calculated according to the coordinate position of the CNV in the chromosome segment, the CN<reference> represents the chromosome copy number in a normal sample, and the CNV<score> represents the whole genome copynumber variation of the DNA sample. The invention also relates to the use of said detection method in the diagnosis of cancer as well as a device for diagnosing cancer conditions.

The invention discloses a genomic-data storage method. The genomic-data storage method includes the steps that in the genome comparison process, gene-sequence comparison information is obtained, and gene-sequence statistical information is established; the gene-sequence comparison information is stored in a magnetic disk, and according to comparison positions of the gene-sequence comparison information in a genome, corresponding indexes are stored in a memory, wherein the indexes are storage positions of the gene-sequence comparison information in the magnetic disk; genome statistical information is classified, and first statistical information and second statistical information are obtained; the first statistical information is stored in the memory, wherein the first statistical information is statistical information with the access frequency higher than the preset frequency in the variation detection process; the second statistical information is stored in the magnetic disk, wherein the second statistical information is statistical information which cannot be stored in the memory and / or statistical information with the access frequency lower than the preset frequency in the variation detection process. The invention also discloses an electronic device with the genomic-data storage method.

The invention discloses the specific gene sequence of fruit anthracnose bacteria and its application. The present invention obtains the specific gene sequence of the fruit anthracnose bacteria based on the whole genome comparison of the fruit anthracnose bacteria and its close relatives, further uses the specific gene sequence to design PCR amplification primers to detect the fruit anthracnose bacteria, and develops related reagents box. The invention can specifically detect C. fructicola, and distinguish it from closely related species such as C. aenigma, C. siamense, and C. musae ; Has the advantages of fast, simple and accurate.

The invention discloses molecular markers, detection primers and detection methods for identifying plantar lactobacillus and pentosus lactobacillus. Specific molecular markers for identifying Lactobacillus plantarum and Lactobacillus pentosus, the nucleotide sequences of which are shown in SEQ ID NO.1, SEQ ID NO.2, SEQ ID NO.3 or 4. The present invention screens new targets for specific molecular detection of Lactobacillus plantarum and Lactobacillus pentosus by using the whole genome comparison analysis technology, and designs primers for the new molecular targets for PCR amplification, which can specifically identify the two target bacteria. Currently, these molecular markers are not available. See report. Compared with 16S rDNA PCR method and physiological and biochemical method, the method established by the present invention has higher specificity, simple operation, short detection cycle, no need for further sequencing, and low detection cost, especially suitable for rapid initial detection of L.plantarum and L.pentosus Sieve provides an important auxiliary identification method for food production enterprises and testing institutions.

The invention discloses a kit for detecting a sudden cardiac death-related SNP on the SCN5A gene related to sudden cardiac death and a detection method thereof, specifically comprising the following steps: 1. Using DNA extracted from a sample as a template to prepare Multiplex PCR and its detection method Purification treatment; 2. SNaPshot single base extension reaction (SBE) and its purification treatment; 3. Capillary electrophoresis of SNaPshot single base extension product and its result analysis; 4. Sensitivity detection. The invention can detect 45 sudden cardiac death (SCD) related SNPs on the SCN5A gene at one time, and obtain clear conclusions. This method no longer utilizes first-generation sequencing and next-generation sequencing technologies for comparison of the whole genome. There is no need for special instruments and methods to screen for genetic background related to sudden cardiac death.

The invention discloses an amplification primer, a screening method and an identification method for identifying olive varieties based on SNP sites, and eight pairs of olive amplification primers. The present invention selects highly reliable and reproducible single-copy fragments through restriction endonuclease digestion, cloning and sequencing, and genome comparison analysis of the leaf DNA of olive varieties, and designs amplification primers for single-copy fragments; and then selects single-copy Fragment-designed amplification primers were used to amplify the leaf DNA of olive varieties by PCR, and 8 pairs of single-copy nuclear gene markers with high amplification efficiency and rich variation were screened out. The amplification products of 8 pairs of olives were relatively pure, with clear peak shapes and no Fluorescent primers are needed, and the detection price is low; 8 pairs of single-copy nuclear gene markers in olive can be used for identification of olive varieties.

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 provides a library building method which comprises the following steps: (1) carrying out splitting decomposition treatment on a paraffin-embedded biological sample, and collecting a nucleic acid sample from a splitting decomposition solution obtained by the splitting decomposition treatment by utilizing a precipitation method, the nucleic acid sample containing a nucleic acid fragment with the length of less than 200bp; (2) carrying out terminal repair on the concentrated nucleic acid and adding a joint so as to obtain a nucleic acid sample connected with the joint; and (3) carrying out amplification treatment on the nucleic acid sample connected with the joint so as to obtain amplification products, and forming the sequencing library by the amplification products. The method is suitable for library building of trace and fragmented nucleic acid samples, the library building success rate can be effectively increased, the read repetition rate of subsequent informatics analysis is effectively reduced, and the genome comparison rate is increased.

The invention discloses a sequencing data processing method and device. Among them, the method includes: splitting the three-generation sequencing data to obtain at least one sub-sequencing data; comparing any sub-sequencing data to the corresponding reference genome to obtain the comparison result corresponding to any sub-sequencing data; For the result, get the merged result. The invention solves the technical problem that a large amount of resources and time are needed to complete the comparison of the genome in the process of genome assembly in the prior art, resulting in slow comparison speed and low efficiency.