77 results about "Tandem repeat" patented technology

The invention discloses an annotation method for analyzing a genome centromere region structure, and belongs to the technical field of biological genes. And prerequisites are needed. The method comprises the following steps: firstly, analyzing repetitive monomers of a centromere sequence based on a heuristic strategy, and judging the centromere sequence; when the serial repetition units are identified, an adjacent matrix is obtained based on serial repetition unit information, the analysis problem of the HORs is converted into a graph theory problem of searching a specific structure in the adjacent matrix, and a sliding window strategy is combined to refine the structure analysis result of the HORs. Compared with the prior art, the method has the advantages that the length of the tandem repeat unit can be detected more accurately, and the defect that two continuous tandem repeat units are identified as a single tandem repeat unit by TRASH is effectively overcome. The method has an obvious efficiency advantage. When a human genome centromere area is analyzed, the method is 10 times faster than a current method while the precision is guaranteed.

Provided are techniques for generating expression products using one or more nucleic acid concatemers that include tandem repeats of a nucleic acid sequence encoding the expression product or products. In one embodiment, different expression products may be co-expressed using a concatemer mixture of a first nucleic acid concatemer and a second nucleic acid concatemer having a predefined ratio to one another.

The invention discloses a preparation method and application of GHK oligopeptide, and belongs to the technical field of biology. According to the method, a nucleotide sequence of the GHK polypeptide is obtained by designing tandem repeat GHK polypeptide ([GHK] 63) and combining preferred codons of bacillus subtilis to optimize a polypeptide coding gene. The GHK oligopeptide is subjected to recombinant expression in bacillus subtilis by utilizing a genetic engineering technology, the obtained recombinant protein is not easy to form an inclusion body and does not contain endotoxin, and the high-yield GHK oligopeptide is obtained after separation, purification and protease digestion treatment. According to the GHK oligopeptide preparation method provided by the invention, extra optimization treatment does not need to be carried out on tandem repeat GHK polypeptides, the yield of the GHK oligopeptide is improved, the whole production process is simplified, the cost is low, and the method is suitable for large-scale production of blue copper peptides and has wide application prospects in the fields of medicines, medical beauty and the like.

Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and / or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

A human sebaceous gland carcinoma cell line and use thereof are provided. The human sebaceous gland carcinoma cell line SHNPH-SeC was deposited in the China Center for Type Culture Collection (CCTCC) on Aug. 31, 2023, with an accession number CCTCC NO: C2023113. The human sebaceous gland carcinoma cell line SHNPH-SeC carries a TP53 mutation, and has been identified as a novel single cell line by short tandem repeat (STR) genotyping. This human sebaceous gland carcinoma cell line exhibits strong adherence and stable cellular characteristics, can be stably passaged for multiple generations, and possesses rapid proliferation and migration capabilities, which are in line with the characteristics of malignant tumor cells.

The present disclosure provides recombinant type XVII collagen having a triple helix structure and uses thereof, which belong to the field of protein engineering technology. The recombinant type XVII collagen has an amino acid sequence formed by tandem repeats of n or more core units, where n is an integer of 1 or more, and the core unit has the amino acid sequence shown in SEQ ID NO: 1. The present disclosure also provides methods for constructing multiple expression systems and methods for preparing recombinant type XVII collagen. provide.

The invention provides a primer group, a kit and a detection method for individual identification of treponema pallidum, the primer group comprises 12 pairs of primers with nucleotide sequences respectively corresponding to SEQ ID NO.1-SEQ ID NO.24. The invention provides a specific DNA fingerprint spectrum of treponema pallidum strains formed by 12 loci, a variable number tandem repeat sequence (microsatellite sequence) of a genome is analyzed, and the specific DNA fingerprint spectrum of the treponema pallidum strains is obtained. The method is used for realizing individual identification of treponema pallidum strains. The primer group provided by the invention has high sensitivity, accuracy and specificity, and the detection method based on the primer group can carry out individual identification, genetic identification and genetic typing analysis at the same time, and has wide application prospects in the fields of population genetics and the like.

This invention provides a method, electronic device, and storage medium for detecting short tandem repeat expansion and genotyping. The method includes the following steps: obtaining third-generation sequencing data and aligning it to a reference genome; extracting STR region sequences based on the coordinate information of the STR in the reference genome and the alignment results; aligning the extracted STR region sequences with a template sequence containing multiple preset STR repeat units and calculating the repeat count; and / or using a method based on adjacent coordinate pairs with the same kmer to calculate the repeat units and repeat counts in the STR region sequences de novo; calculating the repeat count peak using a Gaussian mixture model based on the repeat counts of the STR sequences in multiple reads to obtain the genotyping of the STR in the sample. The method provided by this invention is faster than repeatHMM and also allows for the calculation of the changed repeat unit motif and repeat count when the repeat unit motif changes.

Disclosed herein are methods and systems for determining a score for the copy number of repeat units in a variable number tandem repeat (VNTR) locus in a target polynucleotide. Also disclosed herein are methods and systems for determining the nucleotide sequence of a sample nucleic acid having repeat units, where the methods and systems may utilize the most likely copy number of repeat units determined according to the aforementioned methods and systems. Also disclosed herein are methods and systems for predicting a feature of a subject, wherein the methods and systems may utilize the score for the copy number of repeat units in a VNTR locus in a target polynucleotide determined according to the aforementioned methods and systems.

The present application relates to antibacterial active peptide technology, aiming to provide a kind of Lactobacillus reuteri Small molecule antibacterial peptide and its tandem repeat derivative peptide application.The present application provides the small molecule antibacterial peptide X507 with amino acid sequence as shown in SEQ ID NO.1 and antibacterial peptide X507-4 as shown in SEQ ID NO.2;The latter is the derivative prepared by repeating tandem based on the amino acid sequence of antibacterial peptide X507, which consists of 12 amino acids.The antibacterial peptide and derivative peptide provided by the present application have less amino acids, simple synthesis, low cost, easy industrialization and application;Gram-negative bacteria, gram-positive bacteria and corresponding drug-resistant bacteria growth have broad-spectrum antibacterial activity, good stability, no obvious cytotoxicity advantage, for solving the problem of drug-resistant bacteria infection, promoting green medical treatment and the development of breeding has important significance.

The invention provides a sequencing data error correction method and device, electronic equipment and a storage medium. The method comprises the steps that long-read-long sequencing data are obtained, and the long-read-long sequencing data comprise tandem repeat areas; coding the tandem repeat region and the upstream and downstream sequencing data of the tandem repeat region by adopting a first coding mode to obtain a base continuity characteristic; encoding the upstream and downstream sequencing data of the tandem repeat region by adopting a second encoding mode to obtain upstream and downstream features; and inputting the base continuity feature and the upstream and downstream features into a pre-trained correction model to perform error correction on a tandem repeat region in the long read length sequencing data, thereby realizing combination of the tandem repeat region in the long read length sequencing data and upstream and downstream sequencing data of the tandem repeat region in a depth model. Error correction is carried out on a long-read-length sequencing sequence, so that efficient and universal sequencing data error correction is achieved, the accuracy of sequencing data is improved, and subsequent assembly performance is improved.

This application relates to the biomedical field, specifically to a method for expressing tandem recombinant proteins using *E. coli*. The tandem recombinant protein has the general formula leader peptide-(cleavage site 1-spacer peptide-cleavage site 2-target protein)n, wherein the leader peptide is selected from any sequence of SEQ ID NO:1-4; cleavage sites 1 and 2 may be the same or different, and are double cleavage sites of Kex2 and CPB enzymes selected from dipeptides KR or RR; the spacer peptide is any sequence selected from tripeptide EDG, tetrapeptide SEQ ID NO:5-7, or heptapeptide SEQ ID NO:8; the target protein is GLP-1 or an analogue thereof; and n is a tandem repeat number of 2-10. The inclusion bodies obtained by this method do not require denaturation, and the target polypeptide is obtained through double enzyme digestion. The expression level of the fusion protein can reach 32 g / L, and the yield of the target polypeptide can reach 25.3 mg / g wet cells or 10 g / L fermentation broth.

In one aspect, the disclosed technology relates to systems and methods for determining a length of a tandem repeat region in each haplotype of a diploid genome. In some embodiments, the method may include obtaining paired-end sequencing reads of the diploid genome; aligning the paired-end sequencing reads to a tandem repeat region in a reference genome sequence; classifying each of the paired-end sequencing reads that overlaps the tandem repeat region based on the alignments into a plurality of classes and counting the number of paired-end sequencing reads in each class; providing a set of hypotheses of a length of the tandem repeat region in each haplotype of the diploid genome; and evaluating which hypothesis has the highest likelihood of generating the counted or observed number of paired-end sequencing reads in the plurality of classes to determine the length of the tandem repeat region in each haplotype of the diploid genome.

The present invention provides a polynucleotide comprising, in a 5' to 3' direction, a 5' untranslated region (5'-UTR) and an open reading frame (ORF), wherein the 5'-UTR comprises at least two tandem repeats of the sequence 5'-GCCNCC-3' operably linked to the ORF, where N is any nucleotide. The present invention also provides compositions comprising lipid nanoparticles and polynucleotides, as well as pharmaceutical compositions and their use in medicines, particularly for use as vaccines or in gene therapy.

The invention relates to the technical field of genomics and microbial science, in particular to a myxobacteria T2T genome assembling method. The assembling method mainly comprises the four steps of global assembling, telomere sequence screening, local sequence clustering screening and second-generation data multi-round correction. According to the method provided by the invention, pollution removal strategies of telomere sequence screening and local sequence clustering screening are newly added, so that the problem that tandem repeat sequences in a myxobacteria genome are complex and short is effectively solved, the analysis of a complex region becomes possible, the integrity and continuity of assembly are improved, and the assembly efficiency is improved. The method does not need fingerprint spectrum, Hi-C technology or optical spectrum sequencing technology, reduces the experiment cost, ensures that all the sequences belonging to myxobacteria are extracted, effectively removes the interference of repetitive sequences and deep pronucleus pollution, enables highly similar repetitive sequence fragments to be reduced and positioned to an accurate genome position, and improves the accuracy of the detection result. The integrity and continuity of the genome are obviously improved.

The invention discloses a pH and enzyme dual-response type targeted DNA nano-carrier for relieving tumor cell hypoxia as well as a preparation method and application of the pH and enzyme dual-response type targeted DNA nano-carrier. The DNA nano-carrier comprises m tandem repeat units, each tandem repeat unit comprises a long single-stranded DNA repeat unit, three complementary short single-stranded DNAs and siRNA, each of the three complementary short single-stranded DNA sequences comprises a functional region and a base complementary region, and the functional region is a pH-responsive nucleic acid complementary sequence or a nucleic acid aptamer sequence for specifically targeting cancer cells; siRNA is a gene therapeutic agent for relieving tumor hypoxia, an extended positive-sense strand of siRNA comprises a 5 '-terminal extended pH response sequence and a positive-sense strand, and the 5'-terminal extended pH response sequence is complementary with a pH-responsive nucleic acid complementary sequence of the complementary short single-stranded DNA. The nano-drug carrier has excellent drug loading capacity and targeting property, can deliver anti-cancer drugs such as siRNA in a targeted manner, responds to a slightly acidic / enzyme environment of tumor cells and is quickly released, and the anti-tumor treatment effect is improved.

Nucleic acid preparation and analysis techniques described. In an embodiment, techniques for generating tandem repeats include using adaptor sets having two types of adaptors with respective complementary regions present. When an adaptor of each type is present on end of a nucleic acid fragment, the complementary regions can bind to one another to generate tandem repeats of an insert, e.g., a fragment generated from a target nucleic acid.

This invention provides a novel technique for capturing low-abundance DNA insertion and deletion variants. The capture probe sequence is constructed as 5'-CCGTGGAGAGACCACGG-(F)n-GGCACCAGAGAGGTGCC-3', comprising a 5' stem-loop region, a 3' stem-loop region, and a capture region (F)n between the stem-loop regions. The 5' stem-loop region sequence is 5'-CCGTGGAGAGACCACGG-3', and the 3' stem-loop region sequence is 5'-GGCACCAGAGAGGTGCC-3'. The capture region (F)n is a short tandem repeat fragment, F is the inverse complementary sequence of the inserted fragment or the deletion fragment sequence, and n is the number of short tandem repeats of the F fragment. The DNA insertion and deletion variant capture probe provided by this invention is simple, versatile, cost-effective, efficient, sensitive, and specific. It can effectively capture low-abundance insertion and deletion variant DNA fragments and perform high-throughput capture of unknown insertion and deletion variant DNA fragments, thereby enabling comprehensive and flexible detection of low-abundance insertion and deletion variant DNA fragments.

Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and / or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

The invention belongs to the technical field of bioengineering, and particularly relates to a recombinant XVII type humanized collagen and application thereof. The recombinant XVII type humanized collagen provided by the invention is obtained by selecting two fragments with GPP at two ends of the human XVII type collagen, sequentially connecting the two fragments, and carrying out 8 times of serial reduplication. The recombinant XVII type humanized collagen prepared by the invention not only has the advantages of strong stability, high expression quantity and good hydrophilicity, but also can significantly up-regulate the expression of VEGF gene and WNT10B gene, and has an anti-hair loss effect. Besides, the amino acid sequence of the recombinant XVII type humanized collagen prepared by the invention is 100% the same as that of a corresponding part of natural human XVII type collagen, so that the recombinant XVII type humanized collagen does not generate immunological rejection when being applied to a human body, and has relatively high safety.

To provide antibodies that bind to MUC1* receptor effective to treat or prevent MUC1* positive cancer.SOLUTION: Provided is a human or humanized anti-MUC1* antibody or antibody fragment or antibody-like protein that binds to an extracellular domain site of an MUC1 isoform lacking the tandem repeat region or of a decomposed product.SELECTED DRAWING: None

The invention relates to a group of Y-chromosomal short tandem repeat (Y-STR) markers comprising at least one rapidly mutating (RM) Y-STR marker selected from the group consisting of DYF1000, DYF1001, DYF1002, DYR88, DYS685, DYS688, DYS712, DYS1003, DYS1007, DYS1010 and DYS1012. The invention further relates to a set of amplification primers comprising primers for the amplification of at least one Y-STR marker according to the invention, to methods for amplifying an allele of at least one Y-STR marker, to a kit for identifying an allele of a Y-STR marker by amplification and electrophoretic detection or sequencing detection, and by sequencing of non-amplified DNA, and to the use of the group of Y-STR markers for typing male individuals.

This invention relates to the field of bioinformatics analysis of sequencing data, specifically providing a genotyping method for short tandem repeat sequences based on next-generation sequencing. The detection algorithm considers various positional relationships between sequencing read lengths and STR regions, models each case separately, eliminates the effects of partial sequence mismatches, insertions, and deletions, and integrates all read information to calculate the optimal STR genotyping result that best matches the observation. This method can be used for genotyping detection of short tandem repeat sequences in the human genome.

Nucleic acid preparation and analysis techniques described. In an embodiment, techniques for generating tandem repeats include using adaptor sets having two types of adaptors with respective complementary regions present. When an adaptor of each type is present on end of a nucleic acid fragment, the complementary regions can bind to one another to generate tandem repeats of an insert, e.g., a fragment generated from a target nucleic acid.

Systems and methods for mapping a plurality of sequence reads to a genomic region are provided. A plurality of sequence reads mappable to the genomic region are obtained. An initial Markov model for the genomic region is obtained. The initial Markov model comprises at least (i) a first repeat for a first repeat region, (ii) a second repeat for a second repeat region, and (iii) an intermediate region linking the first repeat to the second repeat. The initial Markov model is refined using the plurality of sequence reads, thereby obtaining a refined Markov model. For each respective sequence read in the plurality of sequences, the respective sequence read is used to find a highest probability path through the Markov model. This highest probability path is then used to map the respective sequence read to the genomic region.

The invention belongs to the technical field of cellular neurobiology, and relates to a method for capturing a dynamic interaction group of fusion protein and intracellular amyloid protein and application of the method. In the capturing method, the fusion protein is formed by fusing tandem repeat amyloid protein and proximity marker enzyme through flexible connecting peptide; through the design of the tandem repeat sequence of the amyloid A beta, the flexible connecting peptide, the proximity marker enzyme and the like, the local multivalence of the protein is remarkably improved, the saturation concentration required by phase separation is further reduced exponentially, more and more lasting liquid condensates can be stably formed in cells, and the phase separation efficiency is improved. Thus, the metastable oligomer droplets formed by the liquid aggregate are stabilized under physiological conditions. Fluorescence bleaching recovery verifies that the agglomerate generated by the method has pathological liquid-solid phase change characteristics (no fluorescence recovery), and successfully simulates the aging process of amyloid protein. The invention provides a powerful tool for researching a phase separation mediated pathogenic mechanism in amyloid protein related neurodegenerative diseases (such as Alzheimer's disease) and screening a therapeutic drug for agglutinate aging or protein hijacking.

The application discloses a method and device for short tandem repeat sequence typing based on third-generation sequencing data and a storage medium. The method for short tandem repeat sequence typing based on third-generation sequencing data provided by the application first extracts all read segments completely covering the short tandem repeat sequence region according to a short tandem repeat sequence site directory; and filters the read segments by average alignment quality to remove low-quality read segments; then calculates the copy number of the short tandem repeat sequence in each read segment, and combines mutation site information of the short tandem repeat sequence to confirm short tandem repeat sequence typing. The method provided by the application can accurately calculate the repetition number of the short tandem repeat sequence, and combines the mutation site to determine the short tandem repeat sequence typing, so that more accurate genotyping results can be provided. Moreover, the method provided by the application is suitable for third-generation sequencing data of different sequencing platforms, has strong applicability, and can maximize the advantages of the third-generation sequencing read length.

The invention discloses a gene expression enhancing element capable of improving a gene transcription level and an application of the gene expression enhancing element. It is found that a delta satellite region from sweet potato mosaic virus (SPLCV) SBG51 comprises a new DNA sequence capable of remarkably enhancing expression of a reporter gene, the gene expression enhancing effect of the delta satellite region does not change polyadenylation of mRNA, the delta satellite region is independent of a promoter and a terminator, and the space-time mode of the promoter is kept. The invention further finds that AT-rich sequences (such as ATAAA or TTAAA or tandem repeat sequences containing a plurality of ATAAA or TTAAA) are key elements of the above effects, even synthetic AT-rich sequences (AT-rich-1 and AT-rich-2) of 29bp are sufficient to increase the expression of the reporter gene GFP by about 3 times, and the gene expression enhancement effect of the AT-rich sequences is well expressed in both plants and yeast cells. Therefore, the invention can be applied to the aspects of improving the activity of the target gene according to the required level, providing high-level and long-lasting protein production and the like.

Methods and compositions for analyzing Tandem Repeats and single nucleotide polymorphisms use unlabeled, allele-specific PCR primers, a quenched fluorescent probe, and blocking nucleic acids which prevent amplification of specific numbers of tandem repeat units.