84 results about "Consensus sequence" patented technology

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 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.

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.

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.

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.

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.

This invention relates to the fields of molecular biology and forensic identification, specifically to a method for bird species identification based on multi-gene co-amplification and nanopore sequencing. The method involves extracting genomic DNA from avian biological samples; using the extracted DNA as a template, amplification is performed using four independent PCR primer pools that specifically target the avian mitochondrial cytochrome C oxidase subunit I gene, cytochrome B gene, 12S rRNA gene, and 16S rRNA gene; after purification of the amplification products, a nanopore sequencing library is constructed and sequenced; finally, bioinformatics analysis, including read length clustering, draft consensus sequence generation, and polishing, is performed on the raw sequencing data to obtain consensus sequences for each target gene. Species identification is then completed by comparing the sequence with a avian sequence database. This method effectively solves the problem that existing technologies cannot simultaneously meet the practical needs of large-scale, rapid, and high-success-rate identification of avian biological samples.

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.

Polynucleotide sequencing generates multiple reads of polynucleotide molecules. Many or all of the reads contain errors. Tracking reconstruction requires multiple reads generated by a polynucleotide sequencer and uses these multiple reads to accurately reconstruct the nucleotide sequence of the polynucleotide molecule. Some reads may contain errors that cannot be corrected. Therefore, there may be reads that can be used over their entire length and other reads with uncertain errors that cannot be corrected. When an uncertain error is discovered, the portion of the read with the error is skipped, and the sequence of the read after the error is used to reconstruct the tracking instead of discarding the entire read. The amount of skipped reads is determined by the location of the subsequence that matches the consensus sequence of other reads after the error. The analysis continues at the location determined by the matched location.

This invention discloses a protein sequence spatial compression and functional optimization method based on a large-scale model, belonging to the fields of artificial intelligence and proteomics. This invention mines potential amino acid substitution sites in consensus sequences and then controls the sequential substitution process using a large protein language model, thereby maintaining the functional stability of proteins during sequence substitution and subsequently screening for substitution combinations that effectively enhance protein function. Introducing a large protein model transforms protein sequences into embedding vectors representing protein structure, function, and physicochemical properties. By analyzing the embedding vectors during the substitution process, it is possible to prevent new proteins from deviating from their original function and basic structure due to substitution. This invention combines consensus substitution identification with large-scale model analysis, effectively compressing the sequence space of amino acid substitutions, thereby significantly improving the efficiency of protein design and modification.

Disclosed are methods of producing recombinant feline morbillivirus (FeMV) using reverse genetics. In some aspects, the methods comprise: (a) extracting FeMV RNA from an isolated FeMV positive sample, (b) generating cDNAs from the FeMV RNA using primers that specifically hybridize to the FeMV RNA, (c) generating cDNA PCR amplicons from the cDNAs using primers that specifically hybridize to the cDNAs to produce cDNA PCR amplicons, (d) amplifying genomic and antigenomic termini of the FeMV RNA by rapid amplification of cDNA ends (RACE) using one or more RACE primers to produce RACE PCR amplicons, (e) purifying the cDNA PCR amplicons of step (c) and the RACE PCR amplicons of step (d) to produce purified DNA, (f) sequencing the purified DNA to produce consensus sequences, (g) assembling the consensus sequences to produce a full-length FeMV genome, and (h) assembling the full-length FeMV genome in a plasmid.

Methods for correcting consensus sequence reads are described. The disclosed methods can comprise: obtaining a sample of double stranded nucleic acid molecules having jagged ends; performing end repair on the jagged ends to introduce jagged end identifiers; preparing a sequencing library comprising the end repaired nucleic acid molecules; sequencing the library to generate sequence reads; mapping the sequence reads to a reference genome to generate a plurality of mapped sequence reads and corresponding sequence information, where the corresponding sequence information includes a jagged end position based on the jagged end identifier, a start position, and a stop position of a given mapped sequence read; grouping the mapped sequence reads into families based on the corresponding sequence information; determining a consensus sequence read for each family; and detecting a biological signal in the consensus sequence read for at least one family of a plurality of families.

Disclosed in the present application are a method for determining a consensus sequence of nucleic acid molecules and the use. The method comprises the following steps: acquiring sequencing information of the nucleic acid molecules, wherein the sequencing information comprises multi-copy sequences of library molecules, and the library molecules comprise single-stranded circular molecules formed by ligation of the nucleic acid molecules and feature fragments; identifying feature sequences of the feature fragments in the sequencing information on the basis of a Levenshtein distance algorithm and by means of known sequences of the feature fragments; dividing the sequencing information according to the feature sequences, and determining repetitive nucleic acid sequences of the nucleic acid molecules; and generating the consensus sequence according to a set of the repetitive nucleic acid sequences of the nucleic acid molecules.

This invention concerns a method for detecting genetically modified organism (GMOs) comprising transgenes and / or detecting genetically modified (GM) material in a sample comprising biological material, comprising performing a nucleic acid amplification reaction on nucleotide sequence elements extracted from an organism or sample with one or more first primer pairs, each of the one or more first primer pairs being specific for a polynucleotide sequence comprised in a transgene or comprised in a consensus sequence derived from an alignment of at least two homologous polynucleotide sequences of a transgene, to produce a first amplicon, and performing a nucleic acid amplification reaction with said extracted nucleotide sequence elements with one or more second primer pairs, each of the one or more second primer pairs being specific for a polynucleotide sequence comprised in a DNA barcode gene suitable for taxonomic identification. A first amplicon obtained from the reaction with the first primer pair is diagnostic of the presence a transgene, and the second amplicon obtained from the second primer pair allows for determination of the taxonomic identity of the organism or the origin of the material derived therefrom in a sample. The invention also concerns primer pairs and diagnostic kits for detecting the presence of GMOs.

A method for planning a well section that includes receiving data that represents a plurality of offset wells. The received data includes an operational sequence of drilling activities that is performed for each of the offset wells. The method also includes generating a consensus sequence based upon the received data, wherein the consensus sequence includes a proposed operational sequence. A dissimilarity score may then be calculated between the consensus sequence and the operational sequence for each of the offset wells and the operational sequence that is associated with the lowest dissimilarity score may then be selected when planning the well section. The dissimilarity score between the consensus sequence and the operational sequence for each of the offset wells may be displayed within a matrix. Any offset wells may be identified as a possible outliers based on the dissimilarity scores then removed from further consideration.

Virus-Like Particles derived from the subfamilies, Parahepevirinae, which infect trout and salmon, and the Orthohepevirinae, which infect mammals and birds, particularly those of the species Paslahepevirus balayani, which can cause acute hepatitis in humans and several mammalian species, and chronic conditions in immunocompromised patients are also disclosed. Major aspects of the invention relate to compositions of Virus-Like Particles comprising viral capsid proteins capable of assembly in cultured cells that may be purified, disassembled, and reassembled in the presence of other molecules suitable for use as therapeutic drug products to facilitate the targeting and delivery of cargo molecules to specific cells or tissues, or as antigenic agents designed to stimulate responses to heterologous epitopes exposed on the surfaces of Virus-Like Particles. Preferred aspects relate to functional capsids comprising polypeptide sequences comprising one or more amino acid substitutions, insertions, or deletions of amino acid encoded by a consensus of ORF2 genes, wherein said variant polypeptides are functionally-similar or have enhanced properties compared to capsid polypeptides encoded by naturally-occurring viruses obtained from clinical samples or prototype Hepatitis E Viruses (HEV). Other aspects include the design and assembly of modified vectors to facilitate the basic and applied studies leading to the development and commercialization of novel drug products, and as tools advancing the interests of institutions involved in animal and human healthcare.

Provided are methods of nucleic acid sequencing. The methods include producing a circularized DNA including a full-length cDNA and a known heterologous sequence, and performing rolling circle amplification using the circularized DNA as template to produce a concatemer including repeating segments including the full-length cDNA and the known heterologous sequence. The methods further include obtaining a raw sequencing read of the concatemer using a nanopore, identifying the repeating segments in the raw sequencing read, and producing a consensus sequence of the full-length cDNA based on the sequences of the repeating segments. Computer-readable media, computing devices, and systems that find use, e.g., in practicing the methods of the present disclosure are also provided.