65 results about "Repetitive Sequences" patented technology

The invention relates to the technical field of genomics, in particular to a gene detection data cleaning method and system based on artificial intelligence. The method comprises the following steps: acquiring gene detection data, and performing preliminary filtering on the gene detection data based on removal of low-quality reads to obtain preliminary filtering data; performing linker sequence identification and removal on the preliminarily filtered data, and performing sequencing error correction to generate gene sequence data; performing GC content analysis and repetitive sequence identification on the gene sequence data to obtain sequence feature data; performing dynamic quality threshold adjustment according to the sequence feature data, and performing secondary filtering on the gene sequence data to generate high-quality sequence data; and performing sequence pattern recognition on the high-quality sequence data to obtain sequence pattern feature data. According to the method, deep analysis is carried out by utilizing sequence characteristics such as GC content and nucleotide distribution, and the recognition capability on sequence complexity and variation modes is improved.

The invention relates to the technical field of biology, in particular to a molecular marker for accurately positioning centromere of chromosome of Chinese trumpet creeper, and the sequence of the molecular marker is as shown in SEQ ID NO.1 and SEQ ID NO.2. The method comprises the following steps: specifically enriching a DNA (Deoxyribose Nucleic Acid) sequence combined with a centromere specific histone CENH3 through a chromatin co-immunoprecipitation technology (ChIP), and sequencing the DNA sequence; sequencing data are analyzed to obtain a centromere sequence of the vicia villosa, and two specific repetitive sequences of the centromere of the vicia villosa are obtained after identification and optimization. Primers are designed according to the sequences, PCR amplification is carried out, amplification product sequences are marked, fluorescence in situ hybridization verification is carried out by analyzing a cytogenetics technology, it is proved that the primers are specifically distributed in a centromere area of vicia villosa, and the centromere specificity of the primers is proved. The marker can be used for genetic identification and accurate positioning of the centromere in genome research, and can also be used for cytological identification of the centromere and karyotype research such as chromosome counting and morphological analysis through centromere signal observation.

Provided herein are non-immunogenic, circular, non-integrating, non-viral DNA vectors, and methods of using such DNA vectors, which are capable of forming one or more specialized secondary structures, for example extended cruciform structures, and express one or more therapeutic genes. These DNA vectors capable of forming one or more specialized secondary structures, for example extended cruciform structures, provide for increased nucleus entry, episomal stability, and long-term transgene expression, and have unique and highly unexpectedly reduced immunogenicity. The one or more specialized secondary structures, for example extended cruciform structures, formed by the circular DNA vectors provided herein are stabilized through the interaction of two specifically oriented repeating sequences, for example AAV-derived inverted terminal repeat (ITR) sequences, separated by a small, non-repeating sequence, for example a non-repeating sequence comprising a small bacterial origin of replication (Ori).

The invention relates to the technical field of molecular biology, in particular to a codon optimization method. The invention provides a codon optimization method, the codon is replaced according to parameters such as codon type and quantity, local GC content, local repetitive sequence, mRNA secondary structure, mRNA free energy and the like, and the optimized sequence can be subjected to experimental screening to obtain a DNA sequence of high-expression protein. The downstream of the method is mainly the application in the IVT mRNA direction: the optimized DNA sequence is constructed into a vector, the plasmid is linearized to serve as a template for in-vitro mRNA transcription, the mRNA is encapsulated into LNP or LNP coupled with other molecules, and the protein expression in 293T cells (not limited to 293T cells) or mice is obviously improved.

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.

The invention belongs to the technical field of biology, and discloses a plasmid system with high rAAV yield and application. The plasmid system of the high-yield rAAV comprises a transgenic plasmid containing two terminal inverted repetitive sequences, a packaging plasmid, an auxiliary plasmid and an shRNA (short hairpin Ribonucleic Acid) expression cassette, the shRNA expression cassette comprises a sequence capable of targeting a target gene in the transgenic plasmid. According to the plasmid system, in the rAAV production process, transcription expression of a target gene is inhibited by expressing a target gene coding region or a target sequence on shRNA targeted transgenic plasmids. The well-designed target sequence is different from human and mammal source gene coding region sequences, and can be applied to various transgenic plasmids in a broad spectrum manner, so that the yield of the rAAV is increased, the rAAV production efficiency of mammal cells can be remarkably improved, and the technical effects of improving the druggability of the rAAV and reducing the production cost are achieved.

To provide a method for determining a stability status of microsatellite loci using a plasma sample from a cancer patient based on next-generation high-throughput sequencing.SOLUTION: A method comprises the following steps: 1) determining length characteristics of repetitive sequences of multiple microsatellite loci in a plasma sample and a MSS plasma sample as a reference sample on the basis of next-generation sequencing method; 2) calculating its corresponding enrichment index Z score for any one of microsatellite loci; 3) summing the enrichment index Z score of all microsatellite loci to calculate the index MS score for determining the status of microsatellites of the sample; 4) calculating a mean and a standard deviation SD of the MS score of the MSS plasma sample as the reference sample, with mean+3SD as the threshold cutoff; and 5) performing determination using the MS score and cutoff.SELECTED DRAWING: None

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.

The present invention provides a cell suitable for gene engineering, cell engineering and cellular medicine, and a method for producing the same. The present invention provides a technique for removing repetitive sequences present in a specific gene region in two or more alleles, thereby facilitating gene targeting or sequencing in the region.

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 an efficient, simple and convenient whole genome CRISPR / Cas9 knockout plasmid library for erencigia parviflora as well as construction and application of the whole genome CRISPR / Cas9 knockout plasmid library, and belongs to the technical field of biology. On the basis of the Eriphaga parviflora T2T genome sequence, a bioinformatics tool is utilized to accurately predict a knockout target spot, double sgRNA is designed to improve the knockout accuracy and efficiency, and meanwhile, the off-target risk is reduced; the method comprises the following steps: synthesizing a double sgRNA-pool chip, amplifying, recovering, connecting a carrier, transforming and the like, so that the phytoneum parvum CRISPR-Cas9 knockout plasmid library which is simple and convenient to operate and high in throughput is successfully constructed. In the double sgRNA design process, advanced tools are adopted to improve the prediction accuracy; after the library is constructed, a strict quality inspection step is also included, so that the library quality is ensured. The invention not only provides a new way for the gene editing of the erencephalium leptosphaerium, but also provides reference for the gene editing of other multi-copy and high-repetitive-sequence biological genes, has obvious effects in solving the off-target problem and improving the editing efficiency and accuracy, and has important scientific significance and application value for the research of functional genomics.

The invention discloses a method for detecting an insertion site of agrobacterium T-DNA on a plant genome, which comprises the following steps: carrying out sequence merging on a T-DNA genome and a plant genome to obtain a merged genome G; performing sequencing read sequence alignment on the combined genome G to obtain an SAM file with an alignment result; performing classification analysis on the SAM file with the comparison result; sequentially carrying out blacklist filtering, merging and repeated area marking analysis on a classification analysis result; and finally outputting the number of the final integration sites and the number of the real integration events. According to the method disclosed by the invention, the sensitivity of T-DNA integration site detection is increased and the false positive rate of detection is reduced by taking measures of considering the special condition of double-end sequencing of an insertion site part, establishing a blacklist, carrying out secondary matching optimization on a specific repetitive sequence of a plant genome, carrying out multi-sequence similarity comparison on a result site and the like.

Provided are guide RNAs and CRISPR / Cas systems that target the C9orf72 gene, lipid nanoparticles or viral vectors comprising such CRISPR / Cas systems, and cells or animals comprising such CRISPR / Cas systems. The invention also provides a method for inhibiting transcription of a transcription start site of a C9orf72 exon 1A and / or inhibiting transcription of a sense and / or antisense transcript containing a hexanucleotide repeat amplification sequence in a C9orf72 gene by using the CRISPR / Cas system, and also provides a method for inhibiting transcription of the C9orf72 exon 1A transcription start site and / or inhibiting transcription of a sense and / or antisense transcript containing the hexanucleotide repeat amplification sequence in the C9orf72 gene. And the use of the CRISPR / Cas system in prophylactic and therapeutic applications for the treatment and / or prevention of diseases associated with amplification of C9orf72 hexanucleotide repeats and / or for ameliorating at least one symptom associated with such diseases.

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 invention discloses a method for judging an unknown exogenous fragment insertion transgenic event based on targeted sequencing, and relates to the field of transgenic technology judgment. According to the invention, the insertion position of a transgenic event can be accurately identified, and even if an exogenous gene is inserted into a repetitive sequence region, transgenic and non-transgenic sequences can be effectively distinguished; the sequencing data after quality control is classified and counted, and a machine learning model is combined to optimize a proportion fluctuation range, so that the accuracy of judging the transgenic event is remarkably improved; the introduction of the Bayesian optimization method can further improve the accuracy and reliability of the model for judging the property of the transgenic event, and avoids the deviation and error in the traditional method.

The invention provides a probe set for detecting the copy number of a TSPAN12 gene and application of the probe set. And the probe group comprises probes of No. 2 to No. 6 exons of the TSPAN12 gene. The probe with extremely high specificity is designed by avoiding a high GC content and a repetitive sequence region, so that a non-specific amplification phenomenon is effectively avoided, pathogenic variations such as point mutation, tiny insertion or deletion and the like of the TSPAN12 gene can be accurately detected, and the possibility of misdiagnosis and missed diagnosis is reduced. The method is especially suitable for TSPAN12 gene detection of familial exudative vitreoretinopathy (FEVR).

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 sequencing data processing method and device, electronic equipment and a storage medium, and relates to the technical field of data processing.The main technical scheme includes the steps that input data are analyzed to obtain splitting parameters, and long read length sequences are screened according to the splitting parameters; based on multi-process local comparison, positioning a non-repetitive sequence in the screened long read length sequence; addressing and positioning repetitive sequences in the screened long-read-long sequences on the basis of a mode of calculating an editing distance by a moving window; and according to the positioning result of the non-repetitive sequence and the positioning result of the repetitive sequence, judging the validity of the long read length sequence. By analyzing the characteristic parameters of the long-read-length sequence, the splitting parameters related to the long-read-length sequence are obtained, matching of repetitive sequences is achieved, and then the success rate of subsequent analysis such as gene comparison and the like is increased.

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.

The present invention provides a cell suitable for gene engineering, cell engineering and cellular medicine, and a method for producing the same. The present invention provides a technique for removing repetitive sequences present in a specific gene region in two or more alleles, thereby facilitating gene targeting or sequencing in the region.

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.