203 results about "Genomic sequencing" patented technology

The invention discloses a crested ibis habitat ecological quality trend analysis method and system, and relates to ecological quality monitoring. The method comprises the following steps: S1, constructing an intelligent sensing network, synchronously obtaining multi-source data of a habitat, identifying activity events of crested ibis, and generating a multi-dimensional habitat parameter table; s2, collecting environmental samples, and generating a microbial functional gene abundance matrix through metagenome sequencing and bioinformatics analysis; s3, taking the activity events of the crested ibis as behavior tags, and generating habitat function health indexes by coupling the parameter table and the matrix training machine learning prediction model; s4, performing spatial interpolation and trend analysis based on the habitat function health index to generate an ecological quality space-time evolution graph; and S5, based on the ecological quality space-time evolution graph, performing quantitative analysis by using a spatial differentiation statistical model, and generating a trend analysis report. By fusing multi-source data, real-time dynamic evaluation of habitat ecological quality and quantitative analysis of driving factors are realized, and a direct decision basis is provided for accurate protection.

The invention relates to the technical field of bioinformatics data processing, in particular to a genome sequence compression method and system. The method comprises the following steps: acquiring genome sequencing data; comparing the sequencing data with a reference genome to determine a difference site; differentiating the difference sites as sequencing errors or real variations through a time sequence difference neural network model; performing differential compression coding according to an identification result; a friendly variation detection format is constructed, and rapid variation query is supported through a multi-level index structure and a variation metadata table. According to the method provided by the invention, the sequencing error and the real variation can be accurately distinguished through the time sequence differential neural network model, and important biological variation information is protected while the compression efficiency is improved by adopting the differential compression coding strategy.

This invention relates to the field of medical testing, specifically to a set of biomarkers, reagent kits, and their applications for diagnosing hypertension in children. This invention involves collecting tongue / intestinal samples from obese children with hypertension, obese children, and healthy individuals, performing metagenomic sequencing, and statistically analyzing the sequencing data using bioinformatics to identify disease-related tongue / intestinal flora. By integrating tongue / intestinal flora with disease information, a combination of flora biomarkers is obtained. A binary classification prediction model constructed using this combination can maximally detect hypertension in obese children.

The invention discloses a genome sequencing sample processing method based on a microdissection technology. The method comprises the following steps: (1) preparing a paraffin section or a frozen section; (2) carrying out HE staining on the section obtained in the step (1); (3) carrying out laser microdissection on nucleic acid; (4) fragmenting the DNA sample, and treating a product obtained in the step (3) by utilizing an ultrasonication method to obtain a DNA fragment; a non-contact ultrasonic crusher is adopted, the power is 80%, ultrasonic treatment is carried out for 10 s, stopping is carried out for 20 s, and 15 cycles are carried out. And (5) carrying out on-machine pretreatment on the genome sequencing sample, wherein the treatment comprises tail end repair and joint connection treatment. According to the method disclosed by the invention, accurate cutting of the sample can be realized, a DNA sample is extracted from a very small amount of cells and a sample for sequencing is constructed, the sample can achieve the same or higher sequencing data quality as that of a traditional method, the usage amount of the cells is greatly reduced, and the repeatability of an experiment is improved.

The invention relates to a method for extracting genome DNA of plants rich in secondary metabolites and a buffer solution, and belongs to the technical field of molecular biology and botany. The method solves the technical problems of low DNA extraction efficiency, poor purity, easy degradation and the like when a traditional DNA extraction method is used for treating plant tissues rich in secondary metabolites such as alkaloid, polyphenol and the like. Comprising the following steps: adding a complexing agent such as polyethylene glycol or polyvinylpyrrolidone when grinding plant tissues in a liquid nitrogen environment; splitting by using a cell wall splitting buffer solution containing dithiothreitol and a nonionic surfactant; carrying out DNA release and extraction at 60-70 DEG C by adopting a CTAB (Cetyltrimethyl Ammonium Bromide) extraction buffer solution containing polyethylene glycol and papain; and then purifying and precipitating to obtain high-purity genome DNA (Deoxyribose Nucleic Acid). The method can effectively remove alkaloid, protein and other impurities, significantly improves the DNA yield and purity, and is suitable for genome sequencing, genetic resource protection, medicinal plant molecular identification and the like of plants with high secondary metabolites such as Stephania kwangsiensis and the like.

The invention provides a capture primer group and a kit for targeted Salivirus genome sequencing and application of the capture primer group and the kit, and belongs to the technical field of genome sequencing. The targeted capture primer group of the Salivirus virus genome comprises a primer 1 and a primer 2, the nucleotide sequence of the primer 1 is as shown in SEQ ID NO. 1, and the nucleotide sequence of the primer 2 is as shown in SEQ ID NO. 2. According to the invention, a universal reverse transcription oligo-T primer and the Salivirus specific primer group provided by the invention are put into the reverse transcription step at the same time, so that not only is a macro transcription effect achieved, but also a Salivirus sequence in a sample is synchronously identified for specific capture. According to the method, the complete Salivirus genome sequence can be efficiently obtained, and the method has good coverage and sequencing adaptability to the virus genome.

The application provides a kind of construction and application for sesbania sesban DNA fingerprint, belong to sesbania molecular marker technical field, the application is based on sesbania genome sequencing, first develops and screens out 8 pairs of SSR primers with sequence specificity and rich polymorphism, by analyzing the agarose gel electrophoresis result of PCR amplification product of SSR primer in different varieties, the assignment of different size, type of PCR amplification product is carried out, to form the DNA fingerprint of each sesbania, the application has the characteristics of easy operation, good repeatability, simple data processing, low cost and the like, and lays a foundation for the classification, identification and utilization of sesbania germplasm resources.

The invention discloses a primer group and method for human metapneumovirus whole genome sequencing and application. Two groups of specific primer pools are designed for the metapneumovirus, totally comprise 21 primers, can effectively amplify the metapneumovirus type A and the metapneumovirus type B, are high in sensitivity and suitable for multi-platform detection, and provide a new direction for detection, typing, traceability and evolutionary analysis of the metapneumovirus.

This invention provides a chalcone isopentenyltransferase gene. GiPT16 This invention relates to the GiPT16 protein, amplification primer set, and applications, belonging to the field of biogenetics technology. It is based on *Glycyrrhiza inflata* (GiPT16 protein, amplification primer set, and applications). Glycyrrhiza inflata Using whole-genome sequencing data and a reverse genetics strategy, the key aromatic isopentenyltransferase GiPT16, involved in the isopentenylation modification of chalcone active ingredients, was successfully identified and functionally characterized. This enzyme was confirmed to specifically catalyze the biosynthesis of psoralen and glycyrrhizin C using DMAPP as a donor. It is the first chalcone isopentenyltransferase characterized in *Glycyrrhiza inflata*, filling a gap in the study of key enzymes in the chalcone isopentenylation metabolic pathway of this species and providing important evidence for further elucidating the molecular mechanisms of quality formation in *Glycyrrhiza inflata* medicinal materials.

This invention discloses methanogenic lyases with the same protein family annotation as PeiR lyases and their applications. These enzymes are obtained through homology screening based on the known characteristics of PeiR lyases targeting peptide bonds in the methanogenic cell wall, using the Pfam protein family database annotation. PeiR lyase proteins participate in the biological process of hydrolyzing archaea cell walls, effectively killing methanogens and reducing methane production. Proteins homologous to this protein have potential methane-reducing potential. This invention integrates rumen microbial metagenomic sequencing data, uses a series of bioinformatics software to screen methanogenic viral proteins, and combines Pfam functional domain annotation for homology analysis, ultimately identifying a series of lyases. These lyases were successfully expressed in a prokaryotic expression system, and in vitro gas production experiments also showed that the crude enzyme solution significantly reduced methane production.

This invention provides a precise quantitative sequencing method based on multi-level atomic structure internal standards, belonging to the field of quantitative metagenomic sequencing technology. The invention first constructs a multi-level atomic structure internal standard system containing at least two concentration levels of internal standard plasmids, forming multiple statistical response units within the same concentration level. After adding the internal standard plasmids to the nucleic acid of the sample, library construction and sequencing are performed. The sequencing signals of the target gene and statistical response units are statistically analyzed, sequencing response parameters are calculated, and consistency analysis is performed on multiple statistical response units within the same concentration level to determine the dynamic limit of detection (LOQ) and to determine the validity of the target gene quantification results. This invention can dynamically determine the LOQ under the current experimental conditions, improving the reliability of quantification results for low-abundance targets.

The invention relates to a primer set for whole genome sequencing of chlamydia psittaci, the primer set comprises a primer subset p1 and a primer subset p2, the primer subset p1 comprises primers with sequences as shown in SEQ ID NO: 1-240, and the primer subset p2 comprises primers with sequences as shown in SEQ ID NO: 241-480. The primer group disclosed by the invention not only can accurately obtain the whole genome sequence of chlamydia psittaci, but also is adaptive to the sequencing modes of all second-generation and third-generation sequencing platforms.

This invention relates to the field of medical technology, specifically to a method for preoperative risk assessment and prediction in liver transplant patients with hepatocellular carcinoma, comprising the following steps: Sample collection: selecting plasma samples and corresponding clinicopathological information from liver transplant recipients of hepatocellular carcinoma, and clarifying the inclusion and exclusion criteria for samples; Plasma cell-free DNA extraction and whole-genome sequencing: extracting and quality-controlling cell-free DNA from the plasma samples collected in step S1, constructing a sequencing library, and performing low-coverage whole-genome sequencing. This invention utilizes plasma-extracted cfDNA for whole-genome sequencing, combined with clinical testing information, to construct a preoperative risk assessment and prediction model for postoperative recurrence in liver transplant recipients of hepatocellular carcinoma based on non-invasive testing. This model can be used to predict the probability of recurrence-free survival before liver transplantation. The model derivation cohort integrates clinical records and circulating tumor DNA data for preoperative recurrence risk prediction.

The invention discloses a primer group and a kit for high-flux targeted detection of pathogens and drug-resistant genes of camel mastitis and application of the primer group and the kit. The primer group consists of 185 pairs of primers with nucleotide sequences as shown in SEQ ID NO: 1-370. According to the primer group, the kit and the detection method disclosed by the invention, specific amplification is carried out on key areas of 20 pathogen target genes and 77 drug-resistant genes of camel mastitis; the kit has the following remarkable advantages: 1) high precision and specificity: sequencing is performed for a specific region, so that the detection accuracy is remarkably improved, low-abundance pathogenic bacterium nucleic acid can be effectively detected, and early diagnosis is assisted; 2) high efficiency and economy: parallel detection of various pathogenic bacteria and drug-resistant genes can be realized through a single experiment, and the detection flux is greatly improved; compared with whole genome sequencing, the cost of targeted sequencing is lower; 3) the method is simple, convenient and universal, the data analysis complexity is remarkably reduced, the method is suitable for various clinical samples such as blood, tissues and secretions, and a unified and efficient detection scheme is provided for different sample types.

Data pipelines for string extraction, clustering, and comparison are disclosed. A method can include extracting sequence regions from each plasmid genome sequence sequenced from a genome of a plasmid based on presence of a fixed flanking sequence marker (FFSM) in the plasmid genome sequence. Each sequence region is within the FFSM and includes a candidate inverted terminal repeat (ITR) sequence. An example method further includes clustering two or more of the sequence regions based on perfect sequence identity to generate clusters; merging two or more of the clusters based on alignments between corresponding sequence regions of the two or more clusters; when a single cluster remains, identifying a genotype of a candidate ITR sequence of the single cluster based on local alignments; and using a plasmid having an ITR sequence with the genotype of the candidate ITR sequence to manufacture a plurality of AAV vectors based on the genotype of the candidate ITR sequence.

The application relates to the technical field of data compression storage, and provides a high-throughput genome sequencing quality score data parallel compression method.The method comprises the following steps: segmenting an original gene sequencing file; performing random sampling and k-mer analysis on the sampling data to obtain statistical characteristic information and establish a parallel sequence partition model for binary classification; splicing two partition files obtained through binary classification according to splicing parameters; predicting the to-be-compressed file through a multivariate linear regression analysis prediction method to obtain compression rate gain and establish a parallel four-level run prediction mapping model for data redundancy elimination; and performing context modeling on two redundancy-eliminated subfiles through a multi-core processor cluster, and performing cascade compression in combination with arithmetic coding to obtain a final compressed file.Under the premise of significantly reducing quality score data compression time and peak memory overhead, the application also improves the quality score data compression rate, reduces the size of to-be-compressed storage files, and saves the construction cost of basic storage facilities.

The invention discloses a primer group and a kit for whole genome sequencing of influenza A virus, and the primer group comprises an external targeting primer with a sequence as shown in SEQ ID NO.1-35 and an internal nested targeting primer of a primer with a sequence as shown in SEQ ID NO.36-89. Based on the primer group, the influenza A virus whole genome detection method is established, sequencing and typing of the influenza A virus whole genome can be completed within 10 hours, a complete genome sequence can be obtained without assembling sequencing data, and compared with a conventional NGS detection technology, the detection method has the advantages that the detection efficiency is greatly improved, and the detection cost is reduced. The accuracy and the stability of influenza A virus detection can be greatly improved.

Methods and systems for processing a plurality of sample reads for genomic sequencing are provided, including, for each sample read of the plurality of sample reads, comparing substring sequences from the sample read to reference sequences representing different portions of a reference genome. One or more reference sequences that match one or more of the compared substring sequences are identified, and a probabilistic location of the sample read within the reference genome is determined based on the one or more identified reference sequences. The plurality of sample reads are classified into a plurality of sample groups based on the determined probabilistic locations of the respective sample reads.

The invention discloses a kit and a method for extracting nucleic acid from an ophthalmic sample and application of the kit and the method in metagenome sequencing. A method of extracting nucleic acid from an ophthalmic sample includes extracting nucleic acid from the ophthalmic sample using a sample processing system comprising the ophthalmic sample, a carrier RNA, protease K, and a lysis reagent. According to the method, a carrier RNA is added to prevent loss of trace nucleic acid, high-concentration protease K is adopted to enhance digestion of protein, and a chemical reagent is adopted to lyse cells, so that excessive damage and degradation of nucleic acid and low-volume elution caused by severe oscillation of mechanical wall breaking are avoided, and the final concentration of nucleic acid is improved.

The invention discloses a broncholung lavage fluid composition for treating non-small cell lung cancer, and relates to the technical field of cancer treatment. The preparation method of the bronchus lung lavage fluid composition for treating the non-small cell lung cancer comprises the following steps: S1, performing metagenome sequencing on a BALF sample, S2, grouping by R / NR based on differential strains obtained in S1 to obtain core bacteria, performing single-strain Kaplan-Meier survival analysis on the strains, and determining the survival rate of the single-strain Kaplan-Meier to obtain the bronchus lung lavage fluid composition for treating the non-small cell lung cancer. Finally, seven key microorganisms, namely bronchopulmonary lavage fluid combinations, which are remarkably related to immunotherapy PFS are locked; s3, determining the relationship between the seven key BALF bacteria and the existing immune therapeutic effect marker; and S4, verifying the generation conditions of IL6, IL8 and RANTES cytokines promoted by the seven strains through an in-vitro cell experiment, and revealing the activation and enhancement effects of the seven strains on immune cell functions. According to the invention, the immunotherapy effect of the non-small cell lung cancer patient can be promoted to be improved by combining a plurality of beneficial specific microorganisms in an airway administration mode. In conclusion, the method has a good application prospect.

The invention belongs to the technical field of gene engineering, and relates to a metagenome extraction method based on different environmental samples. The invention provides a metagenome extraction method based on different environmental samples, and the extraction method provides a similar extraction method aiming at the extraction of microbial metagenomes in different environmental samples, so that the extracted DNA has high quality and high purity and is used for meeting the requirement of metagenome sequencing. The technical problems that various different types of reagents need to be used for different environmental samples, and general integration is difficult are solved.

The present disclosure provides method of whole genome sequencing of microorganisms such as Gram-positive bacteria, Gram-negative bacteria, viruses, and fungi. The various methods comprising steps of isolating nucleic acid from the microorganism and preparing a library of the isolated nucleic acid. Preferably, the methods of whole genome sequencing described herein are automated to provide a robust and efficient sequencing product for various utilities.

The invention discloses a carbapenem drug resistance marker screening method and system based on a cross-species compressed Debrueine diagram and a medium. The method comprises the following steps: starting from whole genome sequencing data of gram-negative bacteria belonging to different species and carbapenem drug phenotypes of the gram-negative bacteria, constructing a compressed Debrueine graph based on cross-species joint data, and taking existence / deletion of nodes in the graph as unified genetic variation characteristics. Performing correlation analysis on the nodes and the drug resistance phenotypes by using a linear hybrid model to obtain a candidate node set related to the phenotypes; k-mer is extracted based on the candidate node sequence, and secondary statistical screening is completed in combination with chi-square test and mutual information; and finally determining a group of carbapenem drug-resistant genetic markers which can be applicable across species through a hierarchical feature selection strategy of random forest and XGBoost. Efficient dimension reduction of large-scale cross-species genome data, cross-species consistent variation representation and high-interpretability marker screening are achieved.

The invention discloses a Candida parapsilosi GDMCC 66465 strain capable of automatically separating and preserving breeds and being used for sausage fermentation and an application method of the Candida parapsilosi GDMCC 66465 strain, and belongs to the field of food microorganisms. The bacterium is screened from Xuanwei hams, can be used for cooperatively fermenting sausages with lactobacillus plantarum, and can be used for remarkably promoting degradation of muscle protein and selective hydrolysis of triglyceride to strengthen the flavor of the hams. GC-IMS detection shows that the content of key flavor substances such as aldehydes and ketones in the finished sausage is remarkably increased, and the flavor score is increased by 30% or above compared with that of a control group. Genome sequencing analysis shows that the strain has no pathogenic risk and is a potential strain suitable for industrial production of fermented meat products.

A system for calculating DNA short-read alignment comprises a memory comprising a plurality of memory cells, the memory comprising first and second regions, a plurality of transmission gates, a plurality of sense amplifiers, each having first and second outputs connected to each bitline in the memory, a plurality of logic gates, each connected to the first and second outputs of each sense amplifier, a digital peripheral circuit connected to the outputs of the logic gates, and a processor configured to perform steps comprising performing a Burrows-Wheeler transform on a nucleotide sequence represented as a string, storing the transformed nucleotide sequence in the first region of the memory, storing a short-read nucleotide sequence in the second region of the memory, activating first and second rows of the memory, and calculating DNA short-read alignment using the digital peripheral circuit.

The present application relates to the field of paternity determination, and provides a non-invasive prenatal paternity relationship determination method and system and electronic equipment, the method comprising: obtaining a paternal DNA sample and a pregnant woman's plasma free DNA sample, the pregnant woman's plasma free DNA sample including a fetal DNA sample; performing genomic sequencing on the paternal DNA sample and the pregnant woman's plasma free DNA sample; after genotype filling, determining the paternal genotype and the fetal genotype; calculating the kinship coefficient of the paternal genotype and the fetal genotype; based on the kinship coefficient of the paternal genotype and the fetal genotype and a pre-constructed corresponding relationship between the kinship coefficient and the paternity relationship, determining the paternity relationship between the father and the fetus. The present application solves the defects of low detection efficiency and high technical cost in the related art, and is convenient to operate, completely non-invasive, and does not cause any physiological interference to the pregnant woman and the fetus; the detection can be carried out from the seventh week of pregnancy, and is suitable for precise identification of the biological father of the fetus and unrelated individuals.

The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5′-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5′- and 3′-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on 5′-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on 3′-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5′- and 3′-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next generation sequencing”).

The application discloses a method for identifying large fragment sequence insertion of a target genomic region and application thereof, and belongs to the technical field of bioinformatics. In view of the problem that large fragment insertion variation is difficult to be accurately recognized in clinical metagenomic sequencing due to short sequencing read length, insufficient coverage and other factors, the application proposes to construct a reference sequence which can represent the insertion variation by means of manual construction, and to realize efficient identification of the insertion event of the target genomic region by combining a short read-based fast alignment process. The method overcomes the dependence of existing structural variation detection tools on high sequencing depth and long read length, has the advantages of fast identification speed, high sensitivity and high accuracy, and is suitable for rapid screening of large fragment insertion related to drug resistance mechanism in clinical samples. Meanwhile, the method can be popularized for insertion variation analysis of other pathogen drug resistance related genes or genomic regions, and has a good clinical application prospect.

The invention relates to the technical field of ocean, in particular to an angiogenic peptide cAMP-137 derived from coral microorganisms and application of the angiogenic peptide cAMP-137. In the invention, the novel angiogenic peptide cAMP-137 is screened and identified from metagenome sequencing data of a coral reef sample of an island in Pacific Ocean for the first time. The angiogenic peptide can significantly inhibit hematoma expansion and stabilize cerebral microvessels in a 10-100 nM therapeutic window, fills the technical blank of existing polypeptide drugs, and provides a new solution for spontaneous and drug-induced cerebral hemorrhage.

The invention discloses a novel smMIP probe, a targeted detection kit and application of the novel smMIP probe. The smMIP probe sequentially comprises a 5'connecting end primer, a UMI molecular tag 1, a sequencing library universal skeleton, a UMI molecular tag 2 and a 3 'extending end primer from 5'to 3', and the universal skeleton comprises two types with the length of 74 nt and 46 nt. The smMIP probe constructed by the invention is suitable for an MGI sequencing platform, the smMIP probe is used for target DNA genome sequencing, the problem that the smMIP is incompatible with an MGI library structure is solved, the utilization rate and the sensitivity of the smMIP probe are improved, and the dependence on a specific platform (such as Illumina) is reduced.