55 results about "Third generation sequencing" patented technology

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 relates to the technical field of information storage, in particular to a DNA-based information storage method. A long sequence in vivo DNA information storage technique is provide. Themain goal is to construct a coding system with strong error correction mechanism based on LDPC and BCH codes, which can reduce the redundancy of primers and indexes by long sequence coding, and achieve a high actual carrying capacity (above 97%). The main goal is to construct a medium-length DNA sequence (above 1Kbp). Saccharomyces cerevisiae in vivo assembly system is used to assemble and store long sequences and preserve information, and the information can be replicated at low cost, high fidelity and high speed by model organisms such as Saccharomyces cerevisiae, Escherichia coli or Bacillus. At the same time, because of the existence of strong error correction system, the data in the bacterial cell can be reduced perfectly with low coverage (1-5 X) in the second generation and third generation sequencing.

The invention relates to a protein molecule electronic device based on a nanopore structure. The protein molecule electronic device is a mono-enzyme biosensor which can be used for detecting a substrate molecule with extremely low concentration in a solution and sequencing the DNA (deoxyribonucleic acid) of the single molecule. The protein molecule electronic device belongs to a third-generation DNA sequencing apparatus. The protein molecule electronic device based on the nanopore structure is characterized in that 1) the solution is divided into two parts by virtue of a solid structure with a nanochannel, wherein the solutions at the two sides of the solid structure are communicated by virtue of the nanochannel; 2) a protein molecule or a protein complex molecule is fixed in the nanochannel; 3) electrodes are respectively put in the two solutions separated by virtue of the solid structure, and resistance of the protein molecule in the nanochannel is detected by detecting current between the electrodes; and 4) the dynamic features of protein conformation are determined according to the changes of a current value passing through the protein molecule, and the information of the protein-catalyzed reaction substrate is obtained.

The invention relates to a method for detecting a fusion gene based on transcriptome sequencing data. The method comprises the following steps of S1: performing second-generation transcriptome sequencing and third-generation transcriptome sequencing on a sample to obtain second-generation transcriptome sequencing data and third-generation transcriptome sequencing data; S2: comparing the third-generation transcriptome sequencing data with a reference genome, identifying FLNC reads possibly subjected to gene fusion and gene pairs possibly participating in fusion, extracting a sequence of the FLNC reads possibly subjected to the gene fusion, and judging a fusion position; and S3: comparing the second-generation transcriptome sequencing data with the FLNC reads possibly subjected to the gene fusion, obtained in the step S2, and identifying the gene pairs fused indeed according to logarithms of discordant paired-end reads and the number of junction reads in a comparison result and the number of the FLNC reads possibly subjected to the gene fusion. According to the method, the fusion gene is detected in combination with third-generation transcriptome sequencing and second-generation transcriptome sequencing, so that a result of detecting the fusion gene in combination with second-generation and third-generation sequencing support evidences is more reliable.

The application discloses a building method of DNA large-fragment library for Pacbio platform and an assay kit. The building method includes subjecting broken DNA large fragments to VII enzyme treatment, sequentially carrying out primary DNA damage repairing and terminal repairing treatment, linker splicing treatment, exonuclease ExoIII and ExoVII double-digest treatment, subjecting products obtained by double-digest treatment to fragment separation through nucleic acid electrophoresis and a fragment recovery system, subjecting products obtained by the fragment separation to secondary DNA damage repairing, so as to obtain the DNA large-fragment library adaptable to the Pacbio platform. According to the building method of the DNA large-fragment library, the whole building process is carriedout without Pacbio library-building assay kit, library building cost is lowered greatly, and a material foundation is laid for promotion and application of the third-generation sequencing and Pacbionucleic acid sequencing platform.

The invention provides a method for detecting expansion of a short tandem repeat. The method comprises the following steps: firstly, carrying out sequence alignment; secondly, detecting short tandem repeat of third-generation sequencing data by RepeatHMM; thirdly, detecting sequence insertion of a short tandem repeat area by inScan; fourthly, calculating an intersection of RepeatHMM detection results and sequence insertion detection results of the short tandem repeat area. According to the method provided by the invention, the results of the sequence insertion and RepeatHMM short tandem repeatdetection are combined, so that the specificity of detecting the expansion of the short tandem repeat is improved.

The invention discloses a gene sequencing data compression and transmission method. The method comprises the following steps of A, establishing a standard DNA sequence database; B, deploying the standard DNA sequence database to a data processing device; C, preprocessing DNA sequencing data: comparing the DNA sequencing data with the standard DNA database one by one, generating a corresponding relationship, replacing an original text of the DNA sequencing data with numbers of the standard DNA database, and separately storing a part, different from the standard DNA database, of the DNA sequencing data; D, performing compression; and E, performing storage or transmission. The standard DNA sequence database is stored in the data processing device, so that a large amount of information contained in the DNA sequencing data can be represented by the numbers of the standard DNA database, and the data capacity after the step of preprocessing the DNA sequencing data is greatly reduced; through further compression, the capacity is smaller, so that the storage space of the DNA sequencing data is smaller, and the data transmission efficiency is higher; and the data in the method is matched with output data of a second-generation sequencing technology and even a third-generation sequencing technology.

The invention provides a third-generation data correction method based on DNA variation detection and belongs to the field of bioinformation technology. According to the method, third-generation sequencing data is processed to serve as reference sequence data, then second-generation sequencing data is compared with the third-generation sequencing data after being processed, and a comparison file is obtained; and variation analytical detection is performed on the comparison file, variation information of the second-generation sequencing data relative to the third-generation sequencing data canbe obtained, and the variation information is utilized to complete correction of the third-generation sequencing data. The DNA variation detection method is applied to third-generation sequencing dataerror correction, the second-generation sequencing data and the third-generation sequencing data are combined in use, and therefore the cost of third-generation data correction is lowered; and a multithread thought is adopted in a program, so that the correction speed of the third-generation data is increased. Through the method, the problems of a high error rate and high cost in a third-generation sequencing technology are solved through a united correction technology, and a foundation is laid for subsequent third-generation sequencing data variation detection.

The invention relates to a method for determining a fetus alpha thalassemia gene haplotype. The method comprises the following steps: establishing a third-generation sequencing library according to ablood sample, wherein the blood sample is collected from blood samples of the father and mother of the fetus; performing the third-generation sequencing for the third-generation sequencing library, and obtaining a third-generation sequencing result; determining a father and mother alpha thalassemia gene haplotype according to the third-generation sequencing result; establishing a second-generationsequencing library according to a detection sample, wherein the detection sample is collected from a peripheral blood sample of a pregnant woman; performing the second-generation sequencing for the second-generation sequencing library, and obtaining a second-generation sequencing result; and determining the fetus alpha thalassemia gene haplotype according to the second-generation sequencing result as well as the father and mother alpha thalassemia gene haplotype.

The invention discloses a nano-structure-based protein unimolecular electronic device and preparation and application thereof; single protein or its complex molecules are fixed to a counter electrode at a nano hole, dynamical features of conformational fluctuation of the protein are characterized by detecting the electrical conductivity of the protein or its complex molecules in a solution, and the activity of the protein and the biochemical reactive process thereof with substrate molecules are detected. The nano-structure-based protein unimolecular electronic device may act as a third-generation sequencing method having great development potential, preparing special DNA sequencing libraries is not required, labeling nucleic acids is not required, ultra-long, continuous, quick and precise base reading can be performed, and ultralow-cost DNA sequencing and otherness can be achieved if a high-throughput molecular device is prepared.

The invention relates to the field of gene engineering, in particular to a reagent for simultaneous extraction of DNA and RNA, a method for simultaneously extracting the DNA and the RNA and application of the reagent. The reagent comprises a natural saccharide compound, a heavy metal salt compound, a neutral salt compound, a thiocyanic acid compound, an alcoholic compound, an organic solvent compound, a phenolic compound, N-lauroylsarcosine and a salt compound used for adjusting the acidity or alkalinity of a solution. The reagent for extracting the DNA and the RNA is optimized, protection to the DNA and the RNA is enhanced, the whole extraction process can be conducted at room temperature, cooling treatment does not need to be conducted, and the needs of follow-up second-generation sequencing and third-generation sequencing can be completely met. The operation method is simple and rapid, the quantity demand of samples is less, and the purity and the concentration of extracted DNA and RNA are high.

The invention discloses a processing method for nucleic acid third generation sequencing raw data and an application thereof. The processing method for the nucleic acid third generation sequencing rawdata includes comparing second generation short sequence data to third generation self-correcting data, obtaining the single-base covering depth of the third generation self-correcting data in a comparison result, shielding an area where the single-base covering depth is lower than the threshold as N, and adopting second generation sequencing hole filling software to fill the shielded area N to obtain the nucleic acid third generation sequencing data with low single-base error rate. According to the processing method for the nucleic acid third generation sequencing raw data, the second generation short sequence data is compared with third generation long sequence data, the second generation sequencing hole filling software is utilized to make up the shielded area N with the low single-base covering depth in the comparison result, the single-base error rate in the third generation sequencing data is effectively reduced, the sequencing quality is improved.

The invention discloses a method and a device for repairing genome sequencing and assembling results, and a storage medium. The method of the present invention comprises the following steps: comparinga genome assembling result to be verified with a Bionano molecular map, finding out areas with unmatched molecular markers or inconsistent lengths, and extending each of the upstream and the downstream of the genome sequence of every area for a preset length to form abnormal areas; respectively analyzing the coverage degrees of the abnormal areas by second-generation data and third-generation data; and repairing the abnormal areas according to the coverage degrees to obtain repaired genome assembling results. The method using a combination of a second-generation sequencing technology, a third-generation sequencing technology and the Bionano map to repair the genome assembling results solves the structural error introduced by the area complexity in genomic splicing in order to prevent excessive loss of the assembling results in structure conflct area operation processing of traditional Bionano verification, and also can process and verify the areas with inconsistent molecular lengths in Bionano and genome assembling results in order to improve the accuracy and integrity of genome splicing.

The invention provides a single-cell transcriptome sequencing method based on third-generation sequencing, which comprises the following steps: (1) carrying out reverse transcription on single-cell RNA by using a reverse transcription primer to obtain cDNA with a bar code; (2) carrying out PCR (Polymerase Chain Reaction) amplification on the cDNA with the bar code, and mixing obtained PCR amplification products with different single cell sources; or mixing cDNA (complementary deoxyribonucleic acid) with barcodes from different single cell sources and then carrying out PCR (polymerase chain reaction) amplification; the reverse transcription primer sequentially comprises an anchoring sequence, a bar code sequence and poly dT from the 5'end to the 3 'end. According to the invention, a bar code sequence is added into a reverse transcription primer to carry out reverse transcription on single-cell full-length RNA; sequences of different single cell sources are marked, DNA amplification products of different sources are mixed to meet the requirement of a third-generation sequencing platform for the template amount, and accurate sequencing of a full-length transcript is achieved through the third-generation sequencing platform.

The invention provides a three-generation sequencing data overlapping detection method and system. The third-generation sequencing data overlapping detection method comprises the following steps: receiving all DNA sequences of third-generation sequencing data, and sorting the DNA sequences according to the length; allocating all DNA sequences to a preset number of parallel threads according to a strategy that the total DNA data processed by each thread is equal in size; for each thread, solving a sub-sequence with the minimum hash value of each window of all DNA sequences and taking the sub-sequence as a minimizer; establishing indexes for all the minimizers according to the hash values, and constructing a reference gene hash index table based on a double-array structure, wherein the reference gene hash index table is divided into two arrays, the index arrays store the storage positions of the minimizers corresponding to different hash values in the structure array, and the structure array stores the position information of the minimizers; and performing DNA sequence overlapping detection according to the reference gene hash index table based on the double-array structure. Sequencing data overlapping detection efficiency can be improved.

The invention relates to a method for determining a fetal beta thalassemia gene haplotype. The method comprises the following steps: constructing a third-generation sequencing library based on a bloodsample, wherein the blood sample is taken from blood samples of fetal father and mother; performing third-generation sequencing on the third-generation sequencing library to obtain a third-generationsequencing result; determining father and mother beta thalassemia gene haplotypes according to the third-generation sequencing result; constructing a second-generation sequencing library based on a detection sample, wherein the detection sample is taken from peripheral blood samples of a pregnant woman; performing second-generation sequencing on the second-generation sequencing library to obtaina second-generation sequencing result; determining the fetal beta thalassemia gene haplotype according to the second-generation sequencing result and the father and mother beta thalassemia gene haplotypes.

The invention discloses a hole filling method and device based on a third-generation sequencing sequence. The method includes the following steps: comparing at least one sub-sequencing sequence contained in a third-generation sequencing sequence to obtain a first comparison result; extracting a sub-sequencing sequence located within a certain range of at least one gap sequence from the first comparison result to obtain at least one first extraction result; performing fine comparison on the first extraction result to obtain a second comparison result; extracting a sub-sequencing sequence located within a certain range of the at least one gap sequence from the second comparison result to obtain at least one second extraction result; assembling the at least one second extraction result to obtain a consistent sequence; and replacing an original sequence in a genome sketch with the consistent sequence, wherein the gap sequence is an unknown sequence. According to the scheme of the invention, the technical problem that in the process of performing genome hole filling on sequencing data, the process of comparing the sequencing sequence has a low speed, and large resource consumption is caused can be solved.

The invention discloses a third-generation sequencing phytoplankton genomic DNA extraction method and application thereof. The method comprises the following steps: (1) adding 18% to 20% (V/V) beta-mercaptoethanol to a buffer GA, then adding zooplankton, and grinding to obtain a tissue buffer solution; (2) adding protease PK to the tissue buffer for digestion, then adding RNase A, allowing standing still, centrifuging to obtain supernatant I, adding a solvent, centrifuging to obtain supernatant II, finally adding a buffer GB, mixing uniformly, and adding anhydrous ethanol to obtain a mixed solution; (3) adding the mixed solution to an adsorbent column CB3, rinsing and eluting to obtain phytoplankton genomic DNA. The method disclosed by the invention is simple, easy to operate, and capableof effectively removing pigments, and obtained phytoplankton genomic DNA fragments are complete, high in purity, and high in concentration, thereby being capable of providing the assurance for smoothimplementation of the third-generation sequencing of zooplanktons, especially cladocerans.

The invention relates to a fetus spinal muscular atrophy gene haplotype determining method and system. The method comprises the following steps of, on the basis of blood samples, structuring a three-generation sequencing library, wherein the blood samples are from parents of a fetus; performing third-generation sequencing on the three-generation sequencing library to acquire third-generation sequencing results; according to the third-generation sequencing results, determining spinal muscular atrophy gene haplotypes of the parents; based on detected samples, structuring a second-generation sequencing library, wherein the detected samples are peripheral blood samples of a pregnant mother; performing second-generation sequencing on the second-generation sequencing library to obtain second-generation sequencing results; according to the second-generation sequencing results and the spinal muscular atrophy gene haplotypes of the parents, determining the spinal muscular atrophy gene haplotypeof the fetus.

The invention relates to the technical field of microbial detection, in particular to a microbial detection system based on a three-generation sequencing technology, which comprises a sample collection device, a sample vibrating device, a sample detection device and a data display device, a test liquid is arranged in the collection device, according to the present invention, an obtained microbial sample is detected by using the third-generation sequencing technology so as to achieve the obtaining of the detection result of the microbial sample; through intelligent identification processing of the detection result, abnormity judgment of the detection result is realized; according to the method, not only is the detection result of the microbial sample obtained, but also the abnormality judgment of the detection result is realized by performing intelligent identification processing on the detection result; and compared with the prior art, the method does not need to culture a microbial sample, and can realize collection of the detection result by adopting the third-generation sequencing technology, so that the time consumed by detection is greatly shortened, and meanwhile, the cost consumed by microbial detection is also effectively reduced.