15 results about "Insertion deletion" patented technology

Provided is a reverse prime editing system, which is used for achieving site-specific and precise small-fragment DNA editing upstream of a target site. In the reverse prime editing system, a targeted strand nickase (such as D10A-Cas9) is used to cleave a nick on a targeted strand, thereby enabling precise small-fragment DNA base insertion, deletion and substitution upstream of the target site under the action of a reverse transcriptase.

Provided is an efficient and precise plant gene knockout method. First, a sequence containing a stop codon cluster is inserted into a genome by means of dual pegRNA to obtain, by means of screening, a stop codon cluster sequence capable of efficiently and precisely knocking out a target gene. A prime editing system and multiple pegRNA programming can be used in combination with the method to enable various genomic modifications such as efficient and precise knockout of one or more target genes, base substitutions, and small fragment insertions, deletions, and substitutions with just one prime editing protein.

The present application relates to the technical field of bioinformatics, in particular to a method for detecting microbial structural variation, mutation and insertion deletion based on second-generation sequencing. The present application is based on the short read Illumina second-generation sequencing strategy, through testing, using the current mainstream biological tools and combining the self-developed program, the automatic analysis of microbial metagenome structural variation (SV), single nucleotide variation (SNV / mutation) and small fragment insertion deletion (Indel) is realized, and the problems of low sensitivity, high false positive rate and low efficiency in the prior art for detecting variation under the metagenome background are significantly solved.

The invention discloses a DNA coding method capable of correcting multiple insertion and deletion errors, which relates to the DNA storage method in the field of data storage. Aiming at the problem of synchronization errors caused by insertion and deletion errors in DNA storage; by utilizing the properties of the generalized Helberg code, a DNA coding method capable of correcting multiple insertion and deletion errors is constructed; at the same time, the expression of ω n+1 in the generalized Helberg code is also deduced to facilitate the calculation of the upper bound of the redundancy value of this coding method.

The application provides an RNA framework for gene editing and a gene editing method, the RNA framework comprising a sequence upstream of a target site, a sequence to be inserted, and a sequence downstream of the target site in the 5' to 3' direction. The gene editing method is based on the inherent mechanism of eukaryotes, uses RNP or RNA (which can be prepared in vitro) and related proteins as carriers, and is transferred into the cytoplasm and nucleus to realize gene editing on a specific sequence or site on the genome of a target system, such as insertion, deletion, replacement and site replacement of a specific sequence, and has high targeting accuracy. The application is more suitable for further clinical application than other prior art because no exogenous system or substance such as protein derived from prokaryotes is introduced, and no double-strand break is generated.

The invention relates to the technical field of coding, and particularly discloses a neural network enhanced base drift type DNA storage error correction coding method. The method comprises the following steps: firstly, mapping binary data into a DNA (Deoxyribose Nucleic Acid) coding unit meeting multi-dimensional biological constraints such as GC (Gas Chromatography) content, homopolymer length, orthogonality and repeated substring, and establishing a coding dictionary (Codebook); insertion and deletion errors introduced in the DNA synthesis, storage and sequencing process are simulated, and detection is carried out through a classification model combining a one-dimensional convolutional neural network and Transform. And for the sequence which is judged to have the insertion / deletion error, comparing a sliding window with a coding dictionary, positioning the error based on an editing distance, and executing base drift type error correction. According to the method, insertion / deletion errors up to 1.1% can be effectively repaired under the condition that no extra error correction code exists, the average decoding time is shortened by about 9% under the 2% error rate, the error correction capability and the calculation efficiency are both considered, and the method is suitable for a large-scale DNA data storage system.

The invention discloses a corn lodging-resistant insertion deletion site and application thereof, and belongs to the technical field of biology. The technical problem to be solved by the invention is how to detect the strength of corn stalks. The lodging-resistant insertion deletion site of the corn, disclosed by the invention, corresponds to nucleotides from the 101 site to the 103 site in SEQ ID No.1 in a sequence table, and is TCC or deletion. Experiments prove that the corn lodging-resistant insertion deletion site disclosed by the invention is related to the stalk strength of corn, and the stalk strength of CC genotype corn of which the 101-103th nucleotides corresponding to SEQ ID No.1 in a sequence table are TCC is lower than that of GG genotype corn of which the 101-103th nucleotides corresponding to SEQ ID No.1 in the sequence table are deleted; the corn lodging-resistant insertion deletion site can be used for corn molecular breeding and breeding of corn with high stalk strength.

This description relates to vectors for the genetic editing of filamentous fungi using the DNA double-strand break repair technique, capable of facilitating repair via homologous recombination, whether through the insertion, deletion or replacement of a DNA segment in the genome. These vectors preferably comprise the sequences defined in SEQ ID NO: 1 and SEQ ID NO: 23.

The invention relates to a DNA sequence alignment method based on deep learning, in particular to a DNA sequence alignment method based on deep learning. The invention aims to solve the problems that the memory occupation is greatly increased, the comparison speed is obviously reduced and the like when an existing mainstream sequence comparison tool such as minimap2 is used for facing an ultra-long DNA sequencing fragment, and the comparison speed is obviously reduced when the problems of high-density structure variation, complex repetitive sequences, relatively long insertion deletion and the like are processed. The problems of insufficient comparison precision and difficulty in comprehensively and accurately reflecting real genome variation characteristics exist in the prior art. The method comprises the following steps of: 1, converting a DNA sequencing sequence into a word vector; 2, inputting the word vectors into a pre-training model, and outputting feature vectors by the pre-training model; carrying out dimension reduction processing on the feature vector; 3, inputting the dimensionality-reduced features into a trained deep learning classification model, and predicting chromosome categories to which sequences corresponding to the dimensionality-reduced features belong; and 4, comparing the sequence of the recorded category with the corresponding chromosome DNA sequence in the reference sequence. The method is applied to the field of DNA sequence alignment.

The invention belongs to the field of gene engineering, and discloses an efficient and accurate plant gene knockout method. The method comprises the following steps: firstly, inserting a sequence containing a termination codon cluster into a genome through double pegRNA, so as to screen a termination codon cluster sequence capable of efficiently and accurately knocking out a target gene; in combination with the method, a guide editing system and a plurality of pegRNA programs are utilized, and various genome modifications such as efficient and accurate knockout, base replacement, small fragment insertion, deletion and replacement of one or more target genes can be realized by only one guide editing protein.

The invention relates to a next-generation sequencing noise reduction method for simultaneously detecting BCR-ABL1 fusion and ABL1 mutation based on RNA and application, and belongs to the technical field of molecular diagnosis. The noise reduction method comprises the following steps: S1, carrying out reverse transcription on total RNA (Ribonucleic Acid) extracted from a leukemia sample to be detected to obtain a cDNA (Complementary Deoxyribonucleic Acid) product; s2, carrying out multiple PCR (Polymerase Chain Reaction) amplification to obtain DNA (Deoxyribonucleic Acid) subjected to PCR amplification; s3, performing linker connection, library construction and next-generation sequencing to obtain DNA library total quantity and sequencing data; and S4, carrying out raw signal filtering analysis, filtering false positive sites in a non-target region and background signals caused by reverse transcription, and synchronously judging a BCR-ABL1 fusion type, an ABL1 kinase region and point mutation and insertion deletion of a BCR gene. The noise reduction method can effectively reduce the interference of the sequencing background, not only expands the detection coverage range, but also has the technical advantages of simplicity and convenience in operation, excellent detection performance, low cost and high throughput.

The invention belongs to the field of gene engineering. The invention relates to a reverse guidance editing system, and particularly, the reverse guidance editing system is used for realizing fixed-point and accurate small-fragment DNA editing at the upstream of a target site. More specifically, according to the reverse guide editing system disclosed by the invention, a nick is cut on a targeting chain by utilizing targeting chain nicking enzyme (such as D10A-Cas9), and accurate small-fragment DNA base insertion, deletion and replacement are performed on the upstream of a target site under the action of reverse transcriptase; as well as genetically modified but non-transgenic organisms and progeny thereof produced by the method.

The invention discloses a non-natural basic group-based multi-insertion / deletion error correction code encoding and decoding method and system, and the method comprises the steps: obtaining a DNA sequence of original data, and carrying out the preprocessing of the DNA sequence, and obtaining a numerical sequence; segmenting the numerical sequence to obtain a plurality of segments of subsequences, encoding each segment of subsequences by adopting an encoding algorithm to obtain a plurality of segments of encoded subsequences, and separating each segment of encoded subsequences by adopting non-natural bases to obtain an encoded sequence; transmitting the coding sequence through an insertion / deletion channel to obtain a receiving sequence; and checking the receiving sequence, judging a subsequence with errors, obtaining a decoding sequence by adopting a differential VT code decoding algorithm, and deleting a non-natural basic group and a redundant bit of a differential VT code in the decoding sequence to obtain a numerical sequence. By inserting the non-natural basic group at the specific position of the DNA sequence, t insertion / deletion errors can be accurately and efficiently corrected, the required redundancy is greatly reduced, and the coding and decoding efficiency is remarkably improved.

The present invention relates to a fusion protein comprising a Cas protein and a bacterial toxin and a use thereof, a fusion protein according to one aspect, a polypeptide thereof, and a CRISPR-Cas system comprising the fusion protein, which can perform efficient base editing. In addition, the size of the polypeptide is small, so that the polypeptide is easy to deliver through a carrier. In addition, when insertion deletion is induced, the insertion deletion efficiency is remarkably improved, when insertion deletion is induced, the insertion deletion efficiency is remarkably improved, and the size of nucleotide forming insertion deletion is also increased, so that the gene knockout can be effectively applied to gene knockout.

Methods and compositions for functional genetic modifications at selected loci are disclosed. The invention also provides cell populations comprising targeted integration of one or more exogenous polynucleotides and / or insertion deletions at one or more selected loci.