34 results about "Repetitive Sequences" patented technology

The invention relates to a primer group, a kit and a method for detecting an ATXN3 gene (CAG) n trinucleotide repetition number, and belongs to the technical field of gene detection. The technical problem to be solved by the invention is to provide the primer group for detecting the n trinucleotide repetition number of the ATXN3 gene (CAG). The primer group comprises a first primer pair and a second primer pair, a forward primer sequence of the first primer pair is as shown in SEQ ID NO. 1, and a reverse primer sequence of the first primer pair is as shown in SEQ ID NO. 2; a forward primer sequence of the second primer pair is as shown in SEQ ID NO. 3, and a reverse primer sequence of the second primer pair is as shown in SEQ ID NO. 4. Through the design of the two pairs of primers, complementary verification is achieved, the detection result is comprehensive and reliable, the technical defects of first-generation sequencing and second-generation sequencing on long-fragment and high-GC-content repetitive sequence detection are overcome, the detection cost is low, the detection period is short, and the primer pair is suitable for clinical detection service.

Methods and systems are provided to identify PCR duplicates of genetic sequence reads using inexact matching. More specifically, clustering of sequence reads based on inexact matching of both positional alignment coordinates and / or molecular barcodes are described. Samples are sequenced to generate unclustered sequence reads associated with a set of sorting features. The unclustered reads are sorted based on a primary sorting feature, and then by the remaining one or more secondary sorting features. In addition to exact matching of the primary sorting feature, unclustered reads that have values of secondary sorting features that fall within a predetermined tolerance distance are clustered together. The clusters are used to identify PCR duplicates which identification may yield a more accurate read of the sample of interest.

This invention discloses a method and application for detecting TA repetitive sequence polymorphisms in the UGT1A1 gene based on nucleic acid mass spectrometry, belonging to the field of biotechnology. The method uses primer sets with sequences as shown in SEQ ID NO. 1-24, 26-36, and 38, where SEQ ID NO. 1-24 are amplification primer sequences for each mutation site, and the remaining primers are single-base extension primers. This invention enables multiplex detection of irinotecan-related gene polymorphic sites based on a nucleic acid mass spectrometry platform, achieving the detection of 12 polymorphic sites in one well, with low detection cost and small sample volume. Furthermore, nucleic acid mass spectrometry technology has advantages such as ease of operation, high sensitivity, high specificity, and high accuracy, while also overcoming the shortcomings of insufficient throughput in qPCR and high cost in sequencing technology.

A method for blind denoising of sequencing data may include receiving a plurality of read sequences associated with a scaffold sequence. Each read sequence may be a repeat of the scaffold sequence, at least one of which is a noisy read sequence that does not match the scaffold sequence. A sequence denoising model may be applied to encode the plurality of read sequences and generate a denoised scaffold sequence corresponding to the scaffold sequence based on the encoding of the plurality of read sequences. The denoised scaffold sequence may be generated without the scaffold sequence. Molecules associated with the scaffold sequence may be analysed based on the denoised scaffold sequence. Related systems and computer program products are also provided.

The invention discloses a CRISPR (clustered regularly interspaced short palindromic repeats) detection system integrating target chain amplification and crRNA synthesis into one tube, and belongs to the technical field of biosensing and molecular diagnosis. The system comprises an annular probe; the annular probe is amplified into double strands by phi29 DNA polymerase after being combined with a target, T7 RNA polymerase transcription is started to generate pre-crRNA, then the pre-crRNA is processed into mature crRNA by Cas12a, an ssDNA amplification product is recognized, an FQ reporter probe is cut, and a fluorescence signal is generated; wherein the sequence of the annular probe comprises a sequence complementary to a target chain, a single-chain T7 promoter sequence and a DNA sequence corresponding to a crRNA repetitive sequence. The detection platform integrates nucleic acid amplification and crRNA synthesis, real one-tube and one-step detection is realized, gRNA does not need to be additionally added, and the detection platform has the advantages of high sensitivity, high specificity, portability in operation and the like.

This invention discloses a system and method for verifying structural variations in genomic repetitive sequences, comprising: a sequence alignment module for aligning sequences in a sorted BAM file, a reference genome's FASTA file, and a VCF file to obtain re-alignment results, which are then sent to a deduplication module; a deduplication module for deduplicating the received re-alignment results and sending the deduplicated results to a structural variation evaluation module; and a structural variation evaluation module for evaluating the received deduplicated results using a distance-based structural variation evaluation method, thereby verifying structural variations in genomic repetitive sequences. This structural variation verification system helps people efficiently, accurately, and comprehensively examine sequencing evidence of structural variations, enhancing and simplifying the manual review process.

The application relates to the field of cytology and relates to an oligonucleotide probe set design for identifying Brassica rapa chromosomes and application, which comprises the following steps: S1: obtaining a NR-TR set in a Brassica rapa R-o-18 reference genome; S2: statistically clustering the NR-TR set and obtaining TR array data of Brassica rapa chromosomes; S3: obtaining a repetitive sequence cluster which is enriched in all the chromosomes of Brassica rapa; S4: segmenting a repetitive sequence representative array of the obtained repetitive sequence cluster; and S5: respectively aligning the segmented sequences to the Brassica rapa R-o-18 reference genome by using blastn. The application establishes a technology for coating Brassica rapa chromosomes, and the technology can batch coat Brassica rapa chromosome materials.

The invention discloses a recombinant PBase transposase, a PiggyBac vector system and a gene recombinant cell constructed by the recombinant PBase transposase and the PiggyBac vector system. The invention provides a recombinant PBase transposase. The amino acid of at least one of the 81st site, the 114 site, the 337th site, the 500th site and the 553th site of a wild type PBase transposase is mutated. According to the invention, the sequence of wild type PBase transposase is improved, codon optimization is carried out according to CHO cell preference, and then the codon optimization is constructed on an expression vector to obtain helper plasmids of a PiggyBac vector system; and connecting a target gene between two terminal inverted repetitive sequences of the expression vector to obtain the transposon plasmid of the PiggyBac vector system. A PiggyBac vector system is transfected into CHO cells, a stably transfected cell strain is constructed in a pressurized screening mode, and cells with high-level expression are obtained after the stably transfected cell strain is used for only 3-5 weeks.

The present invention is in the field of genetic editing tools and methods of genetic endineering. It relates to the engineering of rare-cutting endonucleases designed to contract highly repetitive motives in chromosomes, which are at the origin of certain genetic diseases, in particular the so-called "triplet repeat diseases", such as the Huntington disease. The invention encompasses the method for contracting the repetitive motives, the rare-cutting endonucleases for use to contract repetitive motives in a gene subjected to repeat disorder, the polynucleotides and vectors encoding thereof as well as the resulting pharmaceutical compositions.

Methods and compositions for detecting genetic instability using digital amplification assays. The methods may be performed in a set of isolated volumes and generally may involve competitive hybridization of a competitor and a probe / primer with a normal allele and one or more mutant alleles of a microsatellite locus. The competitor may be configured to compete similarly with, or to outcompete, the primer / probe for hybridization with the normal allele. The primer / probe may be configured to outcompete the competitor for hybridization with various mutant alleles of the locus that alter the length of the repetitive sequence by different amounts. Isolated volumes in which the primer / probe outcompetes the competitor may be enumerated, and represent one or more of the mutant alleles. The methods may enable diagnosing microsatellite instability and treating a subject based on the diagnosis.

The invention discloses a double PCR (Polymerase Chain Reaction) detection kit for trichina and toxoplasma gondii and application of the double PCR detection kit. The kit comprises upstream and downstream primer pairs for detecting trichina and toxoplasma gondii respectively, 2 * Taq Master Mix and non-enzyme water, the primer pair for detecting the trichina specifically aims at a complete sequence of a trichina T1 isolate ISS 003 ribosome small subunit gene, and the primer pair for detecting the toxoplasma gondii specifically aims at a toxoplasma gondii H66R isolate 529REP repetitive sequence region. The duplex PCR detection system disclosed by the invention is good in specificity, and does not generate cross reaction with other common polypide bodies; corresponding target fragments can be amplified when trichina and toxoplasma gondii are detected, and no amplified fragment appears when common pig parasites are detected, so that the specificity is high; the detection limit is 0.10 ng / mu L, so that the kit has relatively high sensitivity. In conclusion, the detection kit disclosed by the invention is high in sensitivity, strong in specificity, mild in reaction condition, short in reaction period and high in detection flux, and can be used for rapidly screening the toxoplasma gondii and trichina in meat products and live pigs in various scenes.

The invention discloses a pegRNA (Ribonucleic Acid) and GRAND editing editing system for specifically recognizing a cattle poll site, and an application of the pegRNA and GRAND editing editing system. Belongs to the technical field of gene editing. According to the invention, on the basis of pilot editing, a GRAND editing editing system is constructed, specific pegRNA and GE-pegRNA expression vectors are designed, a target cattle poll site is realized, the replacement of a 6 bp sequence between 1706055-1706060 bp and a 208 bp sequence between 1705837-1706044 bp of a cattle genome is realized, the bottlenecks that a PE editing system only can insert a fragment less than or equal to 44 bp and the insertion efficiency is low are broken through, and the method has the advantages of high specificity, high specificity, high specificity, high specificity, high specificity, high specificity, high specificity and the like. According to the method, the insertion-deletion mutation of the 202 bp repetitive sequence is realized, the insertion efficiency is improved, and the application scene of a donor-free insertion long fragment sequence gene editing technology is greatly enriched.

This invention discloses a method and kit for quantitative detection of circularized rolling circle amplified miRNAs. The method utilizes T4 RNA ligase to ligate the 3'-OH and 5'-phosphate ends of the target miRNA to form a circular miRNA. Using the circularized miRNA as a template, isothermal rolling circle amplification is performed using phi29 DNA polymerase to generate a large number of single-stranded DNA sequences with repetitive sequences. A universal molecular beacon is used to monitor the fluorescence signal of the amplification products in real time, achieving highly sensitive quantitative detection of miRNAs. This method has advantages such as high sensitivity, high specificity, and a wide linear detection range. It eliminates the need to design specific reverse transcription primers for each miRNA, can be extended to multiplex detection, and is suitable for clinical applications such as early tumor diagnosis, drug efficacy evaluation, and single-cell miRNA expression profiling.

The invention belongs to the technical field of gene editing, and particularly discloses a Crimson fluorescent protein reporting system and application thereof in gene editing efficiency multi-scene evaluation. According to the Crimson fluorescent protein reporting system, an equidirectional repetitive sequence which can be targeted by sgAlb and contains a termination codon is introduced into a Crimson gene sequence, a frame-shift mutant fluorescent reporting module is successfully constructed, and the module can recover fluorescent expression through an SSA (homologous sequence annealing repair) repair mechanism after being cut in a Cas9 / sgAlb system. The developed Crimson report cell system can be used for accurately evaluating the stability and editing efficiency of different sgRNA skeletons; the method is suitable for optimizing a virus transduction system and screening a guiding aid for efficient gene delivery; plasmid pollution in a virus vector system can be rapidly detected, and accurate distinguishing of a functional RNP compound and residual plasmid DNA is realized by comparing the proportion of Crimson positive cells before and after DNase I treatment and heat treatment; and small molecular compounds for promoting homologous directional repair can be efficiently screened.

Compositions and methods for analyzing repetitive sequences in the genome are provided, which are used in methods for large scale analysis of these regions for characterization, detection, and monitoring of human cancer.

Provided are a CRISPR-based imaging system and use thereof. The imaging system comprises: (1) a dCas9-expressing vector or a dCas9 protein; (2) an engineered sgRNA-expressing vector, the engineered sgRNA comprising: a sgRNA backbone containing n copies of RNA aptamer, and a sgRNA sequence specific for a target gene to be detected, wherein n is an integer greater than or equal to 2; and (3) a fusion protein-expressing vector, the fusion protein comprising: an RNA-binding motif specifically recognizing the RNA aptamer, a multimerization peptide and a fluorescent protein, which are operably linked to each other. The imaging system has improved resolution, and achieves labeling and imaging of non-repetitive sequence, especially labeling and imaging of non-repetitive sequence within single-copy gene loci in living cells.

The invention discloses a crop centromere automatic identification method, and belongs to the field of crop centromere identification, and the method comprises the steps: constructing a training set according to a verified CENH3 binding region sequence and a random non-centromere region sequence; extracting multi-dimensional features of the DNA sequence according to the training set; training a CNN-RNN hybrid model according to the multi-dimensional features and obtaining a prediction model used for identifying centromere; and identifying the target genome sequence according to the prediction model to obtain a candidate centromere region. The method does not depend on repetitive sequences any more, and directly utilizes the CENH3 binding characteristics, so that the prediction accuracy is improved. And cross-species application can be realized, so that the general applicability of centromere region identification is improved.

The embodiments herein relate to method and apparatus for phase offset estimation and compensation for Physical Random Access Channel (PRACH) with large frequency offset. In some embodiments, there proposes a method for Physical Random Access Channel (PRACH) preamble detection. The method may comprise the steps ofreceiving a PRACH preamble with a plurality ofrepeated sequences, in which each sequence includes a plurality of elements on a plurality of antennas; performing a phase offset estimation for multiple repetitions within the plurality of repeated sequences, by selectively correlating the multiple repetitions based on magnitudes of the elements; performing a phase compensation for the multiple repetitions, based on the estimated phase offset; performing a sequence combination for the multiple repetitions; and performing a sequence detection on the combined multiple repetitions.

The present invention discloses a method and application for functionalization of engineered DNA crystals after crystallization. The present invention constructs a rigid triangular tensile structural unit, including three different DNA component chains, a total of seven chains, the side chains extending in three double helix directions, and the central chain with three repeating sequences is located in the center of the structural unit. Each double helix structure has two sticky ends with two bases at both ends, which interact with each other to form a very ordered 3D crystal network. T4 DNA ligase is used to connect the sticky ends to obtain stable DNA crystals. The crystal structure of the present invention is stable, the target central chain can be added with complex modifications, and it has universality. The crystal has a wide range of uses in medical disease detection.

This invention discloses a method for constructing sequencing libraries based on blocking primers to remove human nucleic acids, and its application. The blocking primers include blocking primers for binding human repetitive sequences, blocking primers for binding human rRNA sequences, and blocking primers for binding human housekeeping gene sequences. These blocking primers can specifically bind to widely distributed scattered repetitive sequences, rRNA sequences, and housekeeping gene sequences in the human genome. The construction method includes the following steps: constructing a DNA library or an RNA library, or a co-constructed RNA and DNA library; using a library with added sequencing adapters as a template; and performing PCR amplification using adapter primers and blocking primers. The blocking primers can specifically bind to human nucleic acids through annealing and prevent modification by DNA polymerase extension, thus preventing the enrichment of human nucleic acid libraries through PCR amplification, while allowing normal amplification of pathogenic microorganism nucleic acids. This achieves the goal of reducing the proportion of human nucleic acids and provides guidance for pathogen detection.

The present invention discloses a pegRNA, a GRAND editing editing system and an application for specifically identifying the polled site of cattle without horns. The present invention belongs to the field of gene editing technology. Based on the lead editing, the present invention constructs a GRAND editing editing system and designs a specific pegRNA and a GE-pegRNA expression vector, which can target the polled site of cattle without horns, and realizes the replacement of the 6 bp sequence between 1706055-1706060 bp and the 208 bp sequence between 1705837-1706044 bp of the cattle genome, breaking through the bottleneck that the PE editing system can only insert ≤44bp fragments and has low insertion efficiency, realizing the insertion-deletion mutation of the 202 bp repetitive sequence, improving the insertion efficiency, and greatly enriching the application scenarios of the gene editing technology of long fragment sequence insertion without donor insertion.

The invention relates to the field of bioinformatics and genome assembly quality control, in particular to a macrobrachium rosenbergii reference genome structure error correction and quality evaluation method and system. The method comprises the following steps: acquiring a primary assembly sequence and Hi-C data, and constructing a contact matrix and an interaction heat map; and identifying false split sites according to end cross-boundary continuous diagonal interaction, identifying inversion and other topological errors according to bowknot-shaped interaction, and executing merging, splitting and / or redirection to obtain candidate genomes. Global LAI before and after error correction and local LAI with an error correction breakpoint / section as the center are calculated respectively, and combined judgment is carried out by combining BUSCO integrity and a consistency threshold outside the error correction section; and outputting a final reference genome when the global LAI is increased and the local LAI is not reduced and the constraint is met, otherwise, rolling back and replacing error correction. According to the scheme, structure-sequence dual verification is realized, the excessive assembly risk is reduced, and the assembly quality of the repetitive sequence region is improved.

The application discloses a high-throughput transcriptome sequencing library construction method and application thereof. According to the technical scheme of the application, the first level bar code is introduced in the process of reverse transcription to synthesize the first strand of cDNA, so that the different sample libraries can be constructed in parallel in the same experiment. The unique molecular identification code is introduced in the process of reverse transcription to synthesize the first strand of cDNA, so that the repeated sequences generated in the PCR process can be effectively identified and removed. The high-throughput library construction and sequencing are realized by introducing the first level and second level bar codes and by detecting the gene expression level based on the 3' end of the transcript. The application has the gene expression level detection accuracy and expression gene detection efficiency which are equivalent to those of the conventional transcriptome sequencing. Meanwhile, compared with the conventional transcriptome library construction and sequencing, the application has the advantages of high throughput and low cost, and is suitable for large-scale sample gene expression analysis and genotype analysis.

The present invention relates to a guide RNA in which a repetitive sequence cleaved by a process for forming a cascade reaction complex is disposed on the 5'side of a spacer sequence, and a repetitive sequence is not disposed on the 3 'side of the spacer sequence, or a sequence cleaved not by a process for forming a cascade reaction complex is disposed, and a type I CRISPR-Cas system using the guide RNA.

The present disclosure relates to ultrashort peptides capable of forming a gel, to a gel comprising a peptide in accordance with the present disclosure, and to a method of preparing such gel. Such gel is a hydrogel or an organogel. The peptides are suitable bioinks for a bioprinter to build 3D structures through 3D printing as well as other applications.

The invention discloses a single molecule real-time sequencing-oriented assembling method based on a reference genome, and relates to the field of individual genome assembling, in particular to a single molecule real-time sequencing-oriented assembling method based on the reference genome. The method aims at solving the problems that single-molecule real-time sequencing data is high in original error rate, traditional de novo assembly is large in computing resource and memory consumption, and repeated sequences and complex structure variation regions in genomes are difficult to cross. The method comprises the following steps: step 1, constructing a Hash index based on a reference genome; constructing an alignment skeleton of the long read sequence by adopting a staged alignment strategy; recording the comparison skeleton breakpoint of the long read sequence as an SV signal; step 2, clustering is carried out on the SV signals; step 3, constructing a long read sequence overlapping graph; converting the overlapped graph into a directed character string graph and simplifying the directed character string graph; and replacing the reference sequence with the long read sequence comparison information.

The embodiment of the invention provides a hereditary tumor nucleotide polymorphism detection method and device and a storage medium, and the method comprises the following steps: obtaining a read sequence and a reference sequence; the reading sequence and the reference sequence are input into a first detection tool and a second detection tool respectively, and a detection method of the first detection tool is based on a second-generation detection technology and comprises the step of reserving a soft shearing sequence and a repetitive sequence; the second detection tool is based on a third-generation detection technology; and combining the detection results of the first detection tool and the second detection tool to obtain a variation detection result. The problem that defects exist in a second-generation detection technology and a third-generation detection technology in the prior art is solved.

The invention discloses a method for detecting chromatin modification and whole genome information based on single molecule sequencing and application of the method. The invention provides a single molecule long read sequencing platform and a sequencing technology capable of researching protein-DNA interaction under single cell resolution, and the method can accurately analyze epigenetic information such as chromatin modification and the like in a single cell. Comprising histone covalent modification and a binding distribution mode of chromatin binding protein in a genome. According to the construction method of the long-read sequencing library and the single-molecule long-read sequencing data obtained by single-molecule sequencing based on the library, the data can be applied to analysis of repetitive sequences of each copy in a genome and chromatin modification of a'blacklist 'region by analyzing the data.

The invention discloses a masson pine miRNA recognition method based on sRNA sequencing data, and belongs to the technical field of plant bioinformatics. The method mainly comprises the following steps: acquiring original offline data of masson pine sRNA sequencing; performing quality control processing on reads in the original offline data of the sRNA sequencing; converting a file of the high-quality sRNA sequencing data from an FASTQ format into an FASTA format, and combining the repetitive sequences to obtain a combined sRNA sequence; finding out all non-miRNA sequences in the Rfam database, comparing the merged sRNA sequences with all the non-miRNA sequences in the Rfam database by using bowtie according to the standard that one base is mismatched, and reserving the sequences which cannot be compared to form sRNA data in an FASTA format; and continuously performing reference genome sequence comparison, secondary structure extraction, structure filtration, abundance filtration and the like on the sRNA data to finally obtain the miRNA sequence.

The invention discloses a genome assembly method, system and device based on a perl language and a storage medium. The method comprises the steps that a high-precision long-Reads interaction intensity two-dimensional matrix NormalForceMatrix is obtained; the two-dimensional matrix NormalForceMatrix is split, and a clustering result with high precision and long Reads is obtained; and according to the clustering result of the high-precision long Reads, assembling to obtain final results AD and STD. According to the method, a series of bioinformatics means are adopted, sequences measured by single chromosomes are classified into a class group, and the influence of other chromosome repetitive sequences (mainly from telomeres and centromeres) is reduced, so that the assembly complexity of each chromosome is reduced, and the assembly efficiency is improved. The continuity (reflected in the average length of the assembled sequence) of a single chromosome sequence can be effectively improved, and then a genome map with better assembly quality is obtained.