112 results about "Consensus sequence" patented technology

The invention discloses a structure variation merging method based on third-generation sequencing data and considering sequence similarity and a related device. The method comprises the following steps: acquiring single-sample variation data and multi-sample variation data; dividing the single-sample variation data or the multi-sample variation data into different windows by adopting coarse clustering based on a sliding window; fine clustering based on sequence similarity is carried out in each window; combining the fine clustering results; and integrating the combination results to obtain a consensus sequence. According to the method, on the basis of variation length and position information, variation sequence similarity is considered, more similar structure variations can be found, and higher merging precision is achieved.

Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.

The invention discloses a somatic cell structure variation detection method based on a monomolecular long-read length sequence chart hybrid model, which comprises the following steps of: extracting a read length local sequence of a target structure variation interval and a flank region thereof, constructing a local chart genome by utilizing a partial sequence alignment chart algorithm, and encoding a multi-sequence alignment result. And then, a multi-category hybrid model is combined with an expectation maximization algorithm, and clustering analysis is performed on the comparison data, so that the somatic cell structure variation category only from the tumor sample is identified. And finally, generating a consensus sequence of a somatic cell structure variation region in the tumor sample, and taking the consensus sequence as an optimization result of a local genome. Compared with an existing short-read-length sequencing method, the method has the advantages that the problems of comparison errors, low-complexity sequences and genome heterogeneity can be effectively solved, and the detection precision of somatic cell structure variation is remarkably improved. Through the application of a single-molecule long-read-length sequencing technology, more comprehensive and accurate genome information can be provided.

Compressing files is disclosed. An input file to be compressed is first aligned. Aligning the file includes splitting the file into sequences that can be aligned. When splitting the file into sequences or when performing subsequent recursive splitting, the splitting is based on a longest sequence match. The result is a compression matrix, where each row of the matrix corresponds to part of the file. A consensus sequence is determined from the compression matrix. Using the consensus sequence, pointer pairs are generated. Each pointer pair identifies a subsequence of the consensus matrix. The compressed file includes the pointer pairs and the consensus sequence.

The invention provides a viral genome splicing method and system combining a reference sequence and de novo splicing, and the method comprises the steps: carrying out the quality control of the sequencing data of a viral genome sequence, and removing a host genome sequence in the sequencing data based on a k-mers strategy; splicing the sequencing data from the beginning to generate a preliminary assembling sequence of the viral genome; performing virus classification annotation on the virus genome preliminary assembly sequence based on a blastn tool, and selecting a highly similar virus genome sequence from a virus library as a reference sequence according to the virus classification annotation; generating a data set according to the reference sequence and the virus genome preliminary assembly sequence, dividing a plurality of sequence clusters according to the similarity between the sequences in the data set, and generating a consensus sequence; comparing the reads after the host is removed with a consensus sequence, and adjusting the consensus sequence according to a comparison result to obtain a final virus genome sequence. According to the method, the accuracy of virus genome splicing is improved, and the universality is high.

The invention discloses a tiny residual focus detection method and system based on ultra-high depth sequencing, and relates to the technical field of tiny residual focus intelligent detection.The tiny residual focus detection method comprises the following steps that on the basis of a sequencing library, splitting is conducted according to a sample index to obtain a to-be-detected sample, and a consensus sequence is obtained according to a molecular identifier of the to-be-detected sample; based on a consensus sequence, filtering out the consensus sequence of which the mass value is less than 25 or the family size is less than 3, and combining a variation type and a distance from a fragment edge as noise introduced into an original nucleic acid molecular chain; a context sequence (context) and a chain direction are used as noise for introducing the capture level of PCR amplification; on the basis of the noise level, the circulating tumor DNA level is estimated in combination with tumor priori knowledge, and the MRD state is determined by detecting the significance of molecular signal sources. According to the invention, the sensitivity and specificity of MRD detection are improved.

A method for compressing molecular tagged sequence data includes: grouping sequence reads associated with a molecular tag sequence to form a family of sequence reads, corresponding vectors of flow space signal measurements and corresponding sequence alignments, calculating an arithmetic mean of the corresponding vectors of flow space signal measurements to form a vector of consensus flow space signal measurements, calculating a standard deviation of the corresponding vectors of flow space signal measurements to form a vector of standard deviations, determining a consensus base sequence based on the vector of consensus flow space signal measurements, determining a consensus sequence alignment and generating a compressed data structure comprising consensus compressed data, the consensus compressed data including for each family, the consensus base sequence, the consensus sequence alignment, the vector of consensus flow space signal measurements, the vector of standard deviations and the number of members.

The purpose of the present invention is to provide a Bst DNA polymerase that can reduce the effects of interfering substances and reactivity at temperatures lower than the optimum reaction temperature. In addition, the invention aims to provide a reagent composition containing the Bst DNA polymerase, a kit containing the Bst DNA polymerase, and a nucleic acid amplification method using the Bst DNA polymerase. The problem is solved by a Bst DNA polymerase which contains an amino acid sequence represented by SEQ ID NO: 1, or a consensus sequence Asn-X-(Ser / Thr) (X is any amino acid residue other than a proline residue), contains an amino acid sequence having 80% or more identity with the amino acid sequence represented by SEQ ID NO: 1, has 5 '-3' DNA polymerase activity and chain substitution activity, and has a consensus sequence containing an N-binding sugar chain, and the N-binding sugar chain contains more than three mannose residues.

To provide a Bst DNA polymerase capable of reducing the effects of interfering substances and reactivity at temperatures lower than an optimal reaction temperature, to provide a reagent composition and a reagent kit containing the Bst DNA polymerase, and to provide a method for amplifying nucleic acid using the Bst DNA polymerase.SOLUTION: The above problems are solved by a Bst DNA polymerase, which contains a specific amino acid sequence or a consensus sequence Asn-X-(Ser / Thr) (X is any amino acid residue other than a proline residue), contains an amino acid sequence that has 80% or more identity with the specific amino acid sequence, has 5'→3' DNA polymerase activity and strand displacement activity, and contains an N-linked glycan in the consensus sequence, the N-linked glycan containing three or more mannose residues.SELECTED DRAWING: Figure 4

Described herein are methods, systems, and apparatuses for determining a partial consensus sequence of a double-stranded nucleic acid molecule. Both strands of the nucleic acid molecule may be sequenced to generate a sequence of base calls. The base calls may be used to identify sets of concordant and discordant positions. A partial consensus sequence may be generated by using concordant values derived from the concordant positions and discordant values derived from the discordant positions. Also described herein are methods, systems, and apparatuses for determining a consensus sequence of a double-stranded nucleic acid molecule. Both strands of the nucleic acid molecule may be sequenced to generate base calls and quality scores corresponding to each strand. Concordant and discordant positions may be identified using the sequences of base calls. Discordant positions may also use the quality scores and weights. A consensus sequence may be determined using the concordant and discordant positions.

The invention belongs to the technical field of genome structure variation detection, and particularly relates to a method and a system for detecting the variation of a shear interval based on allele perception, an effective high shear signal interval is calculated firstly, then the shear interval is marked, and the variation of the shear interval can be detected more comprehensively; before variation feature comparison, aiming at the condition that the same variation in the shearing interval shows that an inserted or copied variation signal and a shearing signal exist at the same time, or a missing variation signal and the shearing signal exist at the same time, constructing an inserted signal and a missing signal, and performing signal unification, so that a clustering result is more accurate; according to a clustering result in a shearing interval, a consensus sequence is constructed, the consensus sequence is aligned to a reference genome, multi-level information such as a minimap2 alignment result, a new alignment result obtained through re-alignment or read alignment information is comprehensively applied, various types of variation and complex heterozygous variation are comprehensively detected, and the detection capacity of structural variation is improved.

Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.

To provide a practical method for detecting repeat expansion diseases that can comprehensively test for repeat expansion diseases without the need for advanced specialized knowledge in repeat expansion diseases.SOLUTION: The method for detecting a repeat expansion disease according to the present invention includes a library preparation process, a sequencing process, a consensus sequence construction process, a ranking process, and a determination process. In the sequencing process, multiple disease-associated repeat regions and their neighboring genomic regions are designated as target regions, and nanopore sequencing is performed to obtain long-read sequence data for each target region in a subject's genome. In the ranking process, repeat number data for each disease-associated repeat region is compared between a subject and a group of normal healthy persons, and the disease-associated repeat regions in the subject's genome are ranked in the descending order of the possibility of pathological repeat expansion. In the determination process, evaluation is started from the disease-associated repeat region ranked first according to specific steps S1 to S7, and it is determined whether or not the subject has pathological repeat expansion.SELECTED DRAWING: Figure 1

Compressing files is disclosed. An DNA sequence to be compressed is first aligned. Aligning the DNA sequence includes splitting the DNA sequences into smaller sequences or portions that can be aligned. After the DNA sequence is spilt one or more time and aligned, a compression matrix is generated. Each row of the compression matrix corresponds to part of the DNA sequence. A consensus sequence is determined from the compression matrix. Using the consensus sequence, pointer pairs are generated. Each pointer pair identifies a subsequence of the consensus matrix. The compressed file includes the pointer pairs and the consensus sequence.

Systems and methods for determining one or more sequences corresponding to one or more nucleic acid molecules from a plurality of sequence reads are provided herein. In some cases, sequence reads may be obtained and mapped to a reference genomic sequence. Sequence reads may be grouped by one or more features of the sequence reads. The groups of sequence reads may be further grouped to generate one or more subgroups. One or more consensus sequences may be determined corresponding to one or more nucleic acid molecules of a biological sample.

An electrochemical method for measuring the activity of biomarkers using microelectrode arrays functionalized with peptide consensus sequences and redox reporter moieties. Contact of the arrays with a biological sample containing one or more target biomarkers results in cleavage of the peptides and changes the electric current across the array in a quantifiable manner indicating not just the presence of the target biomarker in the sample, but its activity.

The invention belongs to the technical field of virus and gene engineering, and particularly relates to an expression vector of a respiratory syncytial virus (RSV) ON1 genotype consensus sequence strain and an editing strain, a reverse genetic manipulation system and an application of the reverse genetic manipulation system of the respiratory syncytial virus ON1 genotype consensus sequence strain and the editing strain of the RSV ON1 genotype consensus sequence strain and the editing strain of the respiratory syncytial virus ON1 genotype consensus sequence strain. According to the invention, an RSV-ON1 genotype consensus sequence strain is firstly constructed and saved, on the basis, 72 nucleotides which are repeatedly inserted into a G gene of the consensus sequence strain are removed through a gene editing technology, and two strains with different virus G gene sequences are obtained. According to the invention, through construction of RSV infectious clone edited by RSV-ON1 genotype G gene and rescue of the two strains, a fast, simple and accurate RSV reverse genetic system is constructed, and the RSV reverse genetic system can be applied to research on RSV in-vitro virus replication mechanism and pathogenesis and neutralizing antibody immune escape. A etiological technical platform is provided for research, development and evaluation of RSV vaccines, antibodies, drugs and the like.

The present invention relates to a monoclonal mouse IgG antibody against human glycoprotein Ib (GPIb) for therapeutic use for inhibiting a GPIb-mediated activation of platelets, the monoclonal mouse IgG antibody comprising the amino acid consensus sequence tyrosine-valine-methionine (YVM) within the CDR 3 region of the variable domain of the heavy chain.

Human-derived virus-like particles (heVLPs), comprising a membrane comprising a phospholipid bilayer with one or more HERV-derived envelope proteins on the external side; one or more HERV-derived GAG proteins in the heVLP core, and a cargo molecule, e.g., a biomolecule and / or chemical cargo molecule, disposed in the core of the heVLP on the inside of the membrane, wherein the heVLP does not comprise a gag protein, except for gag proteins that are encoded in the human genome or gag proteins that are encoded by a consensus sequence that is derived from gag proteins found in the human genome, and methods of use thereof for delivery of the cargo molecule to cells.

A method for compressing molecular tagged sequence data includes: grouping sequence reads associated with a molecular tag sequence to form a family of sequence reads, corresponding vectors of flow space signal measurements and corresponding sequence alignments, calculating an arithmetic mean of the corresponding vectors of flow space signal measurements to form a vector of consensus flow space signal measurements, calculating a standard deviation of the corresponding vectors of flow space signal measurements to form a vector of standard deviations, determining a consensus base sequence based on the vector of consensus flow space signal measurements, determining a consensus sequence alignment and generating a compressed data structure comprising consensus compressed data, the consensus compressed data including for each family, the consensus base sequence, the consensus sequence alignment, the vector of consensus flow space signal measurements, the vector of standard deviations and the number of members.

The present invention relates to a chimeric influenza virus hemagglutinin (HA) polypeptide comprising one or more stem domain sequences fused to one or more globular head domain sequences, each of the one or more stem domain sequences having at least 60% homology to a stem domain consensus sequence of an H1 subtype HA (H1 HA) and / or an H5 subtype HA (H5 HA), each of the one or more globular head domain sequences having at least 60% homology to a globular head domain consensus sequence of an H1 subtype HA (H1 HA) or an H5 subtype HA (H5 HA).

Methods for generating paired sequencing reads for a polynucleotide, and methods for analyzing paired sequencing reads, are described. Paired sequencing reads can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the paired sequencing reads. Other methods of analysis include using paired sequencing reads to construct or validate a consensus sequence. Paired sequencing reads for a polynucleotide can be generated as follows: by extending a primer with a labeled nucleotide to generate sequencing data for a first region; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein the primer extends through the second region faster than the primer extends through the first region; and generating sequencing data related to the sequence of a third region of the polynucleotide by further extending the primer with a labeled nucleotide.

Compressing files is disclosed. An input, which is associated with an original file and new content, is to be compressed. The input includes a consensus sequence of the original file and the new content. The new content is aligned based using the consensus sequence of the original file in order to generate a new consensus sequence that reflects both the original content and the new content. The compression engine generates a new compression matrix and a new consensus sequence. Using the new consensus sequence, pointer pairs are generated. Each pointer pair identifies a subsequence of the consensus matrix. The new compressed file includes the pointer pairs and the new consensus sequence.

The invention belongs to the field of bioinformatics, particularly relates to a mutation detection method and device and application thereof, and more particularly relates to a low-frequency mutation detection method and device and application thereof. By constructing a new sequence set and combining a single-chain consistency sequence and a double-chain consistency sequence correction method, high mutation detection sensitivity and specificity can be obtained, and meanwhile, due to the fact that more sequences are reserved, the effective amount of data is greatly increased.

DNA is sequenced by (a) independently sequencing first and second strands of a dsDNA to obtain corresponding first and second sequences; and (b) combining the first and second sequences to generate a consensus sequence of the dsDNA. By independently sequencing first and second strands the error probability of the consensus sequence approximates a multiplication of those of the first and second sequences.

Herein is reported a method for selecting a variant of a parental antibody variable domain encoding nucleic acid, wherein the parental antibody variable domain amino acid sequence encoded by said encoding nucleic acid has at least one developability hot spot, the method comprising the steps of (i) providing a multitude of DNA-containing samples (genomic material of antibody secreting B-cell) each including one or more antibody variable domain encoding nucleic acids; (ii) performing PCR amplification of said antibody variable domain encoding nucleic acids of (i) using consensus sequence-specific primers to obtain amplification products (wherein said consensus sequence-specific primers bind to consensus sequences that are common to a plurality of genes within the genetic loci set, thereby generating a pool of amplification products); (iii) sequencing a plurality of said amplification products obtained in step (ii) in order to determine the relative proportion of each nucleotide at each position in a sequencing read; (iv) performing a sequence alignment between the sequencing read results of (iii) and the parental antibody variable domain encoding nucleic acid; (v) performing a sequence-identity / homology-based ranking of the antibody variable domain encoding nucleic acids in said sequence alignment with the parental antibody variable domain encoding nucleic acid being the perfect / template / reference sequence; and (vi) selecting the variant antibody variable domain encoding nucleic acid based on the sequence ranking of step (v), whereby the variant selected in step (vi) is selected so that the developability hot-spot is removed.

To provide a universal vaccine effective against a wide range of influenza virus strains.SOLUTION: The present invention provides a chimeric influenza virus hemagglutinin (HA) polypeptide comprising one or more stem domain sequences, each having at least 60% homology with a stem domain consensus sequence of H1 subtype HA (H1 HA) and / or H5 subtype HA (H5 HA), fused with one or more globular head domain sequences, each having at least 60% homology with a globular head domain consensus sequence of H1 subtype HA (H1 HA) or H5 subtype HA (H5 HA).SELECTED DRAWING: None

The application relates to an anti-apoptosis baculovirus expression vector, which realizes a broad-spectrum anti-apoptosis effect by expressing siRNA targeting a Sf-caspase-1 and Tn-caspase-1 common sequence of Spodoptera frugiperda and Trichoplusia ni insect cells through the vector. The baculovirus vector contains a specific DNA sequence, the DNA sequence contains an siRNA sequence targeting the Sf-caspase-1 and Tn-caspase-1 common sequence transcribed by an RNA polymerase III promoter; the recombinant virus of the vector can express double-stranded small RNA in a host cell, silences the caspase-1 encoded by the host cell through an RNA interference pathway, thereby inhibiting the apoptosis of the host cell, and significantly improving the expression level of an exogenous protein. The application can be used for industrialized production of protein preparations and vaccines.

The present invention provides a plasmid sequencing and sequence correction screening method based on nanopore sequencing and its application, the method comprising: (1) designing barcoded vector primers, performing PCR amplification on plasmid target fragments, mixing PCR amplification products of different plasmid insert fragments into one tube, uniformly building a library for the mixed DNA and sequencing it on a machine, and harvesting a corresponding amount of original offline data according to the number of sequencing samples and the size of the plasmid; (2) implementing data quality control on the original sequencing data based on a sequence correction screening system for high-throughput sequencing, establishing a many-to-one alignment equation between the sequencing sequence and the template sequence, deducing conserved bases through position-specific base frequency statistics, and obtaining a consensus base sequence through sequence recombination; (3) developing a clone screening decision model, judging clones by setting a threshold for the alignment between the consensus sequence and the template sequence, and realizing automated hierarchical screening of clones.

The invention relates to the technical field of DNA data storage, in particular to a DNA information encryption and error correction method based on secondary structure fingerprint separation storage, which comprises an information DNA encoding stage, a structure signature generation stage, a signature DNA encoding stage, an information DNA and signature DNA synthesis stage and a decoding and error correction stage. The information DNA encoding stage is used for encoding original data into information DNA fragments; the structure signature generation stage is used for calculating structure characteristic parameters, generating a compact structure signature, and associating the fragment ID with the compact structure signature to form a signature data set; the signature DNA encoding stage is used for encoding the signature data set into signature DNA fragments; the information DNA and signature DNA synthesis stage is used for respectively synthesizing an information DNA fragment and a signature DNA fragment, and physically separating and storing the information DNA fragment and the signature DNA fragment; and the decoding and error correction stage is used for verifying and correcting the consensus sequence based on the signature data set to recover the original data. According to the method, the structure signature is stored in the independent DNA molecule, so that physical layer encryption protection is realized.