20 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 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 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.

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.

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.

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 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 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 method for realizing wheat whole genome large-scale mutation and germplasm creation by editing repetitive sequences. CRISPR / Cas9 target sites with the copy number higher than 20,000 in wheat genomes are screened, tandem repeat sequences and dispersed repeat sequences are edited in a targeted mode, and heritable large-scale variation, chromosome structure variation and agronomic character variation of the whole genome scale are induced and generated in progeny plants. By editing repetitive sequences, large-scale mutation with chromosome and subgenome specificity can be realized, the created mutant library not only provides heritable variation mutant types different from those of traditional physical and chemical mutagenesis methods, but also generates materials such as chromosome aneuploidy (such as monosome, tetrasome and whole-arm deletion) and the like. And a unique genetic resource is provided for wheat functional genomics research and germplasm improvement.

The invention discloses oligonucleotide for treating NOTCH2NLC gene related diseases and application of the oligonucleotide, and provides an oligonucleotide molecule which can be specifically hybridized in a region containing GGC repetitive amplification of a NOTCH2NLC gene or a transcript of the region, and can regulate and reduce the expression of a GGC repetitive sequence. The specific binding position of the oligonucleotide molecule and the NOTCH2NLC gene is positioned on the upstream of the GGC repetitive sequence of the NOTCH2NLC gene, and corresponds to the 149390685 to 149390719 position of a GRCh38 / hg38 reference genome; or the downstream of the GGC repetitive sequence of the NOTCH2NLC gene corresponds to the position 149390857 to the position 149390882 of the GRCh38 / hg38 reference genome. According to the invention, a plurality of oligonucleotide molecules with NOTCH2NLC specificity are creatively designed and synthesized from a DNA level and an RNA level, a GGC repetitive sequence of a specific targeting NOTCH2NLC gene is realized, translation of the GGC repetitive sequence is blocked, generation of toxic polyG protein is inhibited, and a new method and approach are provided for gene therapy of NOTCH2NLC gene related diseases.