172 results about "Nanopore sequencing" patented technology

The invention provides a construction method of a bacterial pathogen detection model based on nanopore adaptive sampling and deep learning, and a method, equipment, a medium and a program product for detecting bacterial pathogens by applying the model, and relates to the technical field of nanopore sequencing. The bacterial pathogen detection method comprises the following steps: obtaining a water sample to be detected; and inputting a to-be-detected water sample into the detection model constructed in the invention to obtain a detection result of the to-be-detected water sample. The sensitivity and the accuracy of pathogen detection are obviously improved, and the improvement on prevention and control of water-borne diseases is facilitated.

The invention discloses a pathogenic microorganism detection system based on nanopore sequencing and intelligent interpretation. The system comprises six modules including a biomolecule electric signal acquisition module and a pathogen characteristic sequence extraction module. Ion current change signals are collected through a nanopore chip array, a pathogen characteristic sequence is extracted through differential coding, a hypergraph topological structure self-adaption building module is used for building a pathogen relation model, a multi-dimensional heterogeneous pathogen parameter fusion analysis module integrates morphological parameters, metabonomics parameters and other multi-dimensional parameters, and the multi-dimensional heterogeneous pathogen parameter fusion analysis module is used for analyzing the multi-dimensional parameters. The optimized hypergraph neural network reasoning module realizes pathogen category prediction, and finally, the nanopore sequencing result intelligent interpretation output module generates a detection report containing pathogen categories, subtypes and risk levels. The system is combined with nanopore sequencing and an intelligent algorithm, pathogenic microorganism detection can be efficiently and accurately completed, the accuracy, reliability and efficiency of detection are greatly improved, and the requirement for rapid and accurate detection of pathogens in practical application is met.

The invention is suitable for the technical field of gene sequencing, and provides a nanopore sequencing signal identification method and system based on Transform, and the method comprises the following steps: carrying out normalization processing on a nanopore sequencing signal, and segmenting the nanopore sequencing signal into signal windows with fixed lengths; signal features are extracted through a Transformer encoder comprising a convolutional layer and a multi-head self-attention module; generating a prediction probability of a current base through a cross attention mechanism by adopting an autoregressive Transform decoder and combining the signal features and context information of a decoded base sequence; iteratively generating an optimal base sequence based on a beam search algorithm, and optimizing decoding efficiency in combination with key value cache; and carrying out overlapping region fusion and quality control on a segmented decoding result, and outputting a final sequence. According to the method, the precision and reliability of nanopore sequencing in complex biological sequence analysis are remarkably improved, and the recognition accuracy on multiple gene sequencing data sets is higher than that of an existing CTC-based model.

The invention discloses a primer composition and a kit for identifying testudinate species and application of the primer composition and the kit. The primer composition comprises primers (SEQ ID NO.1-6) for targeted amplification of specific marker genes 16S, COI and Cytb of testudinate mitochondrial species and an enrichment universal primer (SEQ ID NO.7). According to the invention, full lengths of three mitochondrial genes 16S, COI and Cytb are taken as targets, a specific primer group added with an enrichment tag and an enrichment primer are designed, and a targeted nanopore sequencing method capable of realizing testudinate species identification is established and optimized, and the method can simultaneously capture testudinate mitochondrial species specific marker gene information of a family species level, and can be used for identifying testudinate species. The problem that the existing DNA bar code is difficult to accurately identify the testudinate species due to the lack of database information is effectively solved; and each marker gene can obtain a complete coding sequence, so that genetic information is richer, and the method can be used for geographical traceability analysis of testudinate species.

The invention discloses a species identification kit for animal mitochondrial bar code multiplex PCR amplification and nanopore sequencing, and relates to the technical field of species identification. The species identification kit comprises optimized primer pairs aiming at four hyper-variable genes (Cytb, COI, 16S rRNA and 12S rRNA) of mitochondria, by introducing R, Y, D and other degenerate bases at key sites, the binding capacity of the primers and template DNA of different species is remarkably improved, the problems that an existing universal primer is prone to mismatch, low in efficiency and even failed in amplification during cross-species amplification are solved, and the species identification kit has the advantages of being high in specificity, high in specificity and high in specificity. The method can be used for species identification of a mixed DNA sample containing at least two different animal species sources. The species identification primer combination is applied to preparation of an animal species identification kit, and the detection coverage range of the kit is expanded. According to the animal species identification method provided by the invention, a multiple PCR amplification system and a nanopore length reading sequencing technology are combined, congeneric sibling species with highly similar sequences can be distinguished, and the method has good accuracy.

The application relates to a sarcoma fusion gene nanopore sequencing primer set and application thereof, wherein the primer set comprises five pairs of specific primers (Primer 1-5) with fixed sequences, each primer follows the design principle of 18-25 bp in length, 40%-60% in GC content and strict matching of a target sequence at a 3' end, and the length of an amplification product is 300-800 bp, which is suitable for nanopore sequencing. Through qPCR verification, the primer set has single-peak melting curves, close-to-100% amplification efficiency, strong specificity and excellent amplification performance.

A combination of lipid-binding molecules and / or lipid-binding proteins with lipid components (i.e., mispids) is provided for use in modifying the interaction between target molecules and lipid membranes. This includes, for example, the use of lipid-binding molecules and / or mispids to improve the sequencing efficiency and throughput of nanopore-based sequencing systems. To sequence target molecules such as nucleic acid sequences or nucleic acid substitute polymers derived therefrom, lipid-binding molecules and / or their mispids are combined with the target molecules. The mixture is then applied to a nanopore-based sequencing chip. The target molecules are then sequenced in the presence of lipid-binding molecules and / or nanodiscs, thereby improving the capture, arrival time, and effective concentration of the target molecules across the chip membrane. Such improved efficiency is particularly beneficial, for example, when the concentration of the target molecule is low.

The disclosure describes sequencing workflows and reagents used in those workflows that are suitable for sequencing a target nucleic acid using a nanopore sequencing device. The disclosure also describes detergent and air-flow based methods and compositions used to clean a device pre- and post-sequencing to enable reuse of a consumable device in a nanopore sequencer.

The invention discloses a detection system and method for identifying mycobacteria and drug resistance genes of the mycobacteria based on nanopore sequencing, and relates to the field of biological medicine, the detection system comprises a specific targeted enrichment module, a nanopore sequencing module and a biological information analysis module; the specific targeted enrichment module comprises a probe combination, and the probe combination covers a mycobacterium tuberculosis complex conservative identification gene, species-specific genes of common nontuberculous mycobacteria and mycobacterium leprosy, and full-length or partial sequences of drug resistance related genes in a targeted manner; by utilizing the characteristics of nanopore length reading length and real-time sequencing and a tuberculosis specific targeted enrichment strategy, accurate identification of a mycobacterium tuberculosis complex group, synchronous typing of 42 mycobacteria, analysis of 24 drug-resistant genes, and efficient detection of structural variation and low-abundance heterogeneity drug-resistant mutation are realized, the detection period is shortened, the detection cost is reduced, and the detection efficiency is improved. And a comprehensive and reliable technical basis is provided for accurate diagnosis and treatment of mycobacterium infection.

The invention discloses an HLA (human leukocyte antigen) gene amplification primer based on a nanopore sequencing platform and a typing method, and relates to the technical field of gene engineering, the amplification primer comprises an HLA-A gene amplification primer pair: a forward primer HLA-A-F5; a reverse primer HLA-A-R5; an HLA-B gene amplification primer pair: a forward primer HLA-B-F3; a reverse primer HLA-B-R3; the HLA-DQB1 gene amplification primer pair comprises a forward primer HLA-DQB1-F7, a reverse primer HLA-DQB1-F7 and a reverse primer HLA-DQB1-F7; a reverse primer of HLA-DQB1-R7; the HLA-DRB1 gene amplification primer pair comprises a forward primer HLA-DRB1-F1, a reverse primer HLA-DRB1-F2, a reverse primer HLA-DRB1 A reverse primer (HLA-DRB1-R1); the HLA-DRB3 gene amplification primer pair comprises a forward primer HLA-DRB3-F6, a reverse primer HLA-DRB3-F6, a reverse primer A reverse primer (HLA-DRB3-R8); by designing the specific amplification primer group and combining with the nanopore sequencing length reading technology, the problems of insufficient resolution and the like of the existing typing technology are solved, the typing accuracy and resolution are improved, and the performance is superior to that of the traditional technology; meanwhile, the process is optimized, the limitation of long detection period and the like is broken through, the whole process is rapidly completed, the technical threshold and detection expenditure are reduced, high efficiency, convenience and economy are considered, and support is provided for clinical popularization and scientific research application.

The disclosure relates to nanopore preparations with reduced concentrations of detergents including detergent-free preparations. The disclosure provides lipid nanoparticles (LNPs) comprising a lipid, saposin, and a nanopore, methods for producing such LNPs, as well as systems and methods for nanopore-based sequencing using such LNPs. The new nanopore preparation avoids the pitfalls of using detergent-based compositions, such as disrupting the interactions between a target molecule and a nanopore during sequencing, disruption of the lipid bilayer, and batch-to-batch variability in nanopore preparations.

The invention relates to a novel HfaB nanopore protein mutant and application thereof in sequencing, and belongs to the technical field of nanopores. The polynucleotide for coding the nanopore protein mutant and the recombinant expression vector can express the nanopore protein mutant, and can be used for constructing recombinant cells or recombinant strains for expressing the nanopore protein mutant. The wild-type nanopore protein provided by the invention has relatively high pore stability and is suitable for nanopore sequencing, the sequencing current property of the nanopore protein mutant obtained by modification on the basis of the wild-type nanopore protein is further improved, the sequencing precision is obviously improved, the sequencing signal amplitude and step number are obviously increased, the pore current stability is enhanced, and the nanopore protein mutant can be applied to nanopore sequencing. The spontaneous blocking condition is reduced, and the abnormal noise on the via hole signal is reduced.

Provided are a method for constructing a nucleic acid library and a nanopore sequencing method. The method for constructing a nucleic acid library comprises: processing ends of a double-stranded target nucleic acid to obtain an end-processed product, the end-processed product containing a first end and a second end, and the first end and the second end each containing a terminal overhang sequence; and directionally ligating a first adaptor and a second adaptor to the first end and the second end of the end-processed product, respectively, to obtain a nucleic acid library, the first adaptor being different from the second adaptor. The method is capable of addressing the problems of a low proportion of effective double-stranded sequencing sequences and low efficiency in double-stranded sequencing libraries constructed in the existing technology, and is applicable to the field of nucleic acid library construction.

The invention provides a method and a device for simulating a pulsed field gel electrophoresis band based on a sequencing technology. The method for simulating the pulsed field gel electrophoresis band based on the sequencing technology comprises the following steps: acquiring nanopore sequencing data of a biological sample to be analyzed, and assembling based on the nanopore sequencing data to obtain a genome sequence; according to the sequence characteristics of the restriction endonuclease, identifying a restriction enzyme cutting site corresponding to the restriction endonuclease from the genome sequence; when the restriction enzyme cutting site is the restriction enzyme cutting site subjected to methylation modification, removing the restriction enzyme cutting site to obtain a residual restriction enzyme cutting site; calculating the distance difference between two adjacent restriction enzyme cutting sites according to all residual restriction enzyme cutting sites, and taking the distance difference as the molecular weight of a simulated band; aiming at the molecular weight of each simulated strip, determining a strip position corresponding to the molecular weight; and drawing a simulated pulse field gel electrophoresis band result according to the position of each band and the molecular weight corresponding to the band position so as to accurately simulate the band result.

The invention provides a method for performing nanopore sequencing by using a sealer. According to the method disclosed by the invention, the sequencing library can only be combined in the capture range of the nanopores, the library is efficiently captured by the nanopores in the sequencing process, and the utilization efficiency of the library is improved.

The invention discloses a ganoderma lucidum binuclear genome assembly method based on haplotype analysis, and belongs to the technical field of bioinformatics. The purpose of the present invention is to overcome the accuracy and accuracy of high hybrid genome assembly. The invention provides a ganoderma lucidum binuclear genome assembly method based on haplotype analysis, which comprises the following steps: obtaining mononuclear ganoderma lucidum cells, respectively carrying out whole genome sequencing by utilizing Illumina NovaSeq, Nanopore, Hi-C and PacBio HiFi, and obtaining accurate genome information according to the sequencing data of the Illumina NovaSeq and the sequencing data of the Nanopore. And an assembly strategy of haplotype separation is realized.

Provided are a method for representing a target biomolecule, a ligation method or a preparation method for a sequencing library, an activation linker, a method for preparing the activation linker, a kit for nanopore sequencing, and a use of the activation linker in nanopore sequencing.

The present inventive concept relates to methods of nucleic acid sequencing, and applications and uses of the same. Aspects of the inventive concept include nanopore sequencing on nucleic acids, such as ribonucleic acids (RNAs), including, but not limited to, transfer RNAs (tRNAs). Further aspects include kits for performing the methods, and applications of the methods of the inventive concept as substantively described herein.

A sequencing method may include generating a construct comprising the polynucleotide and a complement of the polynucleotide. The construct may be disposed through the aperture of a nanopore. A first plurality of measured values may be generated corresponding to the sequence of the polynucleotide. A second plurality of measured values may be generated corresponding to the sequence of the complement. A sequence of the polynucleotide may be generated using the first plurality of measured values and the second plurality of measured values.

Some embodiments of the methods and compositions provided herein relate to nanopore sequencing of a target polypeptide. In some embodiments, a sequencing substrate is prepared by Edman degradation from a target polypeptide immobilized on a substrate. De novo sequencing is performed with the sequence substrate and a nanopore embedded in a membrane.

The invention provides a real-time drug sensitivity analysis system and method based on nanopore sequencing, pathogen enrichment treatment is carried out on a collected clinical sample, and then nanopore sequencing is carried out to identify a target pathogen and a plurality of drug-resistant gene loci of the target pathogen; determining a sequencing data quality index of each drug-resistant gene locus according to the sequencing coverage depth, the average base quality value and the independent read length support number of each drug-resistant gene locus, the drug-resistant gene loci with the sequencing data quality indexes between a primary early warning threshold value and a final judgment threshold value in the dynamic threshold values serve as drug sensitivity analysis loci, and the drug-resistant confidence score of each drug sensitivity analysis locus is determined according to the sequencing data quality index and the sequencing error rate of each drug sensitivity analysis locus. And generating a final drug sensitivity analysis report. By adopting the scheme provided by the invention, real-time drug sensitivity analysis can be carried out on the clinical sample under the conditions that the proportion of pathogen nucleic acid in the clinical sample is low and the sequencing data quality dynamically fluctuates.

Disclosed herein is a modified oligonucleotide, the modified oligonucleotide comprises one or more modifications in at least one of a phosphate backbone, a nucleobase, or a sugar. The one or more modifications impede translocation through a nanopore by increasing non-covalent interactions with the interior of the nanopore or the lipid bilayer that supports the nanopore, increasing the bulk size or the steric hinderance of oligonucleotide, or alter the charge density of the oligonucleotide.

This disclosure relates to novel nanoporous proteins and their applications in sequencing, belonging to the field of nanoporous technology. The nanoporous proteins provided in this disclosure enable the observation of resolvable DNA perforation signals, can be used for nanoporous sequencing, and enrich the variety of nanoporous proteins. The mutant proteins obtained after modification show significantly increased expression levels, a marked improvement in spontaneous blockage, and solve the problem of difficulty in assembling into bilayer membranes. They exhibit uniform electrophysiological properties, stable pore currents, relatively high sequencing accuracy of DNA perforation signals, and outstanding sequencing current properties.

The invention relates to the technical field of bioinformatics, and discloses a base recognition method and device for nanopore sequencing and a storage medium. The method comprises the following steps: inputting current data obtained by nanopore sequencing into a pre-trained convolutional neural network model to obtain current feature data; inputting the current feature data into a pre-trained encoder model to determine an attention score of the current feature data, and determining a semantic vector based on the attention score; the encoder model has a multi-head self-attention structure to calculate an attention score, and the multi-head self-attention structure fuses the rotation position codes to fuse the position dependency relationship between different positions in the attention score; inputting a semantic vector output by the encoder model into a CTC decoder model to obtain a base recognition result; the method not only can be applied to identification of DNA molecules, but also can be applied to identification of RNA molecules, and the universality of the base identification method can be improved while the accuracy of base identification is improved.

The present application discloses triblock copolymer (TBC) molecules having a modified chemical head moiety. The triblock copolymer is a poly (2-methyl-2-oxazoline)-poly (dimethyl siloxane)-poly (2-methyl-2-oxazoline) (PMOXA-PDMS (Polydimethylsiloxane)-PMOXA) copolymer, and the copolymer is a copolymer of poly (2-methyl-2-oxazoline)-poly (dimethyl siloxane)-poly (2-methyl-2-oxazoline) (PMOXA-PDMS-PMOXA). The head group moiety comprises an azide or a triazole. The TBC molecules are useful as components in polymeric vesicles, vesicle, and membrane compositions, such as components in synthetic membranes for use in nanopore sequencing devices. Methods of making the modified TBC molecules and methods of use are also disclosed.

The application discloses a nanopore sequencing chip, a preparation method thereof and a packaging structure, and relates to the fields of micro-nano processing, advanced packaging and biological medicine. The nanopore sequencing chip comprises a first insulating layer, a second insulating layer and an electrode, the second insulating layer is arranged on the first insulating layer, a plurality of holes arranged in an array are arranged on the second insulating layer, the holes penetrate through the second insulating layer and are in communication with the first insulating layer, the electrode is arranged at the bottom of the holes, a hydrophobic area is arranged on the second insulating layer, the hydrophobic area is located above the holes and is arranged around the holes, and a hydrophilic modified area is arranged at the bottom of the holes. The preparation method is simple, the light diffraction characteristics can be utilized, and a double-layer structure can be prepared by only one photoetching exposure technology. The packaging structure adopts a metal lead and a leadless packaging form, the crosstalk problem of the metal lead is solved, and separate transportation is adopted, so that the shelf life is prolonged. The nanopore sequencing chip has the advantages of simple structure, low cost and good stability.

A sequencing method may include generating a construct comprising the polynucleotide and a complement of the polynucleotide. The construct may be disposed through the aperture of a nanopore. A first plurality of measured values may be generated corresponding to the sequence of the polynucleotide. A second plurality of measured values may be generated corresponding to the sequence of the complement. A sequence of the polynucleotide may be generated using the first plurality of measured values and the second plurality of measured values.

Disclosed in the present disclosure are a sequencing adapter, a sequencing adapter complex, a method for multiple amplifications of a target nucleic acid sequence, and a method for nanopore sequencing. The sequencing adapter includes a first strand and a second strand. The first strand sequentially includes, from the 5' end to the 3' end, a sequencing guide sequence, a helicase binding sequence, a restriction structure, a first complementary sequence, and a first primer sequence; the restriction structure prevents a helicase from moving; the first strand has a 3' free end; the second strand sequentially includes, from the 5' end to the 3' end, a second complementary sequence, and a constraining sequence or a sequence complementary to the nucleic acid sequence of the constraining sequence; the constraining sequence includes the nucleic acid sequence modified with a hydrophobic molecule at an end; the first complementary sequence is reversely complementary to the second complementary sequence, and the sequencing adapter is formed by annealing the first strand and the second strand; and the sequencing adapter further includes a structure that prevents the second strand from being displaced by a polymerase. The sequencing adapter and sequencing adapter complex of the present disclosure are simple in construction process, and high in yield.

The utility model discloses a molecule detection unit and a chip. The molecule detection unit comprises a substrate, a first structural layer, a second structural layer, a sensing electrode, a third structural layer, a first buffer solution flow channel, a sample flow channel, a single-hole liquid storage cavity, a liquid resistance flow channel and a second buffer solution flow channel, the liquid resistance flow channel and the single-hole liquid storage cavity are arranged in the first structure layer, and the bottom of the single-hole liquid storage cavity is communicated with one end of the liquid resistance flow channel; the sample runner is arranged in the second structural layer and is communicated with the single-hole liquid storage cavity; the first buffer solution runner is arranged in the third structural layer; the bottom of the second buffer solution runner is communicated with the other end of the liquid resistance runner, and the top of the second buffer solution runner is communicated with the first buffer solution runner; the sensing electrode is arranged at the communication position of the single-hole liquid storage cavity and the liquid resistance flow channel. According to the invention, the arrangement density of the nanopore device in unit area can be improved, the chip manufacturing efficiency is improved, and the flux of the nanopore sequencing device is improved.