40 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.

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.

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 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 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.

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.

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.

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.

The present disclosure generally relates to providing accurate genotypes for high-repeat genes. First, the repeat structure of sequencing reads is identified, and sequence reads with abnormal repeat structures are removed to generate a first dataset. The sequence reads of the first dataset are filtered to remove sequences with structural artifacts to generate a second dataset. The data from the second dataset is input into a model to generate a third dataset containing sequencing reads classified by allele. Next, a consensus sequence is generated for each allele in the third dataset, generating a fourth dataset of consensus reads for all alleles included in the third dataset. Each allele in the fourth dataset is translated to generate a fifth dataset containing amino acid sequences corresponding to each allele. Then, the state of a variant that alters a protein is determined based on the amino acid sequences in the fifth dataset.

A consensus sequence of the antigen telomerase (ConTRt) can be generated and used in preventive and therapeutic vaccination. The consensus sequence of telomerase was generated by the fusion of two sequences, one belonging to human telomerase (hTERT) and the other to dog telomerase (dTERT), with the aim of developing an effective vaccine for the treatment of tumors expressing both human and dog telomerase, hence in both the human and veterinary sectors.

The invention discloses a method, a system, equipment and a medium for assembling third-generation sequencing data based on clustering and graph construction, and belongs to the technical field of biological sequence processing. The method comprises the following steps: obtaining sequence similarity based on third-generation sequencing data, and clustering sequences by using a clustering algorithm to obtain different clusters; assembling the sequences in the same cluster based on a graph construction method to obtain an intra-group consensus sequence; and combining all intra-group consensus sequences from different clusters, and assembling based on the graph construction method to obtain an inter-group consensus sequence. According to the technical scheme, through the strategy of sequence clustering, intra-group assembly and inter-group assembly, the assembly complexity is effectively reduced, the accuracy and integrity of the consensus sequence are ensured through the optimal overlap graph algorithm and depth pruning, and the method has remarkable technical advantages.

The invention relates to chimeric influenza vaccines. 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 which has at least 60% homology with a stem domain common sequence of HA (H1 HA) subtype and / or H5 HA (H5 HA) subtype, the one or more globular head domain sequences each have at least 60% homology with a globular head domain common sequence of H1 subtype HA (H1 HA) or H5 subtype HA (H5 HA).

The invention discloses an accurate sequence analysis method and system based on nanopore length and read length sequencing data. The method comprises the following steps: comparing nanopore sequencing data with a reference genome through a minimap2 algorithm, and screening out high-quality long-read-length sequences in a target area and specific upstream and downstream ranges; extracting a target area local sequence of each read length, calculating an editing distance matrix, performing Box-Cox transformation, performing clustering analysis by adopting a Gaussian mixture model, and determining an optimal clustering number through a BIC criterion; performing multi-sequence alignment and polishing on each type of sequences to generate a high-precision consensus sequence; and finally, recognizing homologous conserved sequence fragments through re-comparison and global comparison, and outputting candidate sequences for targeting PCR (Polymerase Chain Reaction) primer or CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) sgRNA design. According to the method, the problem of high error rate of nanopore length and read length data can be effectively solved, the accuracy and reliability of sequence analysis are improved, and reliable technical support is provided for precise gene editing and molecular diagnosis.

Polynucleotide sequencing generates multiple reads of a polynucleotide molecule. Many or all of the reads contain errors. Trace reconstruction takes multiple reads generated by a polynucleotide sequencer and uses those multiple reads to reconstruct accurately the nucleotide sequence of the polynucleotide molecule. Some reads may contain errors that cannot be corrected. Thus, there may be reads that can be used throughout their entire length and other reads that have indeterminant errors which cannot be corrected. Rather than discarding the entire read when an indeterminant error is found, the portion of the read with the error is skipped and the sequence of the read following the error is used to reconstruct the trace. The amount of the read skipped is determined by the location of subsequence after the error that matches a consensus sequence of the other reads. Analysis resumes at a location determined by the location of the match.

The present invention relates to an NP antigen peptide of the SFTS virus, the NP antigen peptide including a novel mutation. NP protein sequences of 56 strains collected from the entire genotype were analyzed, consensus sequences of NP proteins were derived therefrom, and then an NP peptide antigen incorporating an amino acid substitution mutation and having improved structural stability was designed through structural analysis modeling. As a result of evaluating immunogenicity and protective ability using an SFTS virus vaccine composition prepared using the NP peptide antigen, it was found that a vaccine composition comprising the NP antigen of the present invention has an excellent ability to produce an immune response and an excellent ability to protect against SFTS virus infection, and thus the NP antigen peptide according to the present invention can be used in a vaccine composition for severe fever with thrombocytopenia syndrome.

The P450 monooxygenase derived from Spongiibacter sp IMCC 21906 is subjected to molecular modification by utilizing a protein engineering rational design method, a mutant of which the enzyme activity and the thermal stability are simultaneously improved is obtained through consensus sequence analysis and FoldX virtual saturation mutation screening, the enzyme activity is improved by 14.25 times compared with that of an original enzyme, and the half-life period of the P450 monooxygenase at 45 DEG C is prolonged by 4.6 times. A reasonable strategy is provided for improving the activity and the thermal stability of the P450 monooxygenase by utilizing a directed evolution technology, and a basis is provided for industrial application of the P450 monooxygenase.

Provided are a vaccine composition for pan-COVID-19 comprising a consensus sequence of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants.

The application provides a seasonal influenza virus vaccine strain recommendation method and system based on variant adaptability, comprising: obtaining influenza virus hemagglutinin protein HA sequence data and influenza positive rate data from the current influenza season to the last three influenza seasons; identifying amino acid mutations at each site of the HA protein sequence, screening risk mutations for the next influenza season; searching the HA protein sequence of the current influenza season for sequences containing risk mutations, and grouping sequences carrying completely consistent risk mutations into the same risk variant; calculating the product of the conditional probability of the independent component branching ability, immune escape ability and transmission ability of the risk variant as the risk variant adaptability; taking the risk variant with the highest adaptability score as the dominant variant for the next influenza season; determining the HA protein sequence corresponding to the dominant variant, determining the consensus sequence, and selecting the strain corresponding to the HA protein sequence with the highest similarity to the consensus sequence as the candidate vaccine strain for the next influenza season.

Virus-Like Particles derived from the subfamilies, Parahepevirinae and Orthohepevirinae, 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 disclosed. Compositions of VirusLike 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 are provided. Functional capsids comprising polypeptide sequences comprising amino acid substitutions, insertions, or deletions of amino acid encoded by a consensus of ORF2 genes, that 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) are provided.

Disclosed in the present invention are a xylose-inducible transcription factor component and a use thereof. The xylose-inducible transcription factor component comprises: a xylose-inducible transcription factor XlnR derived from a filamentous fungus and a binding consensus sequence of the xylose-inducible transcription factor XlnR. By combining the transcription factor XlnR with a prokaryotic xylose-inducible transcriptional repressor XylR, a dual-regulated inducible system obtained exhibits an extremely low leakage level, but maintains a maximum activation level comparable to that of an XlnR single-regulated xylose-inducible system. The present invention solves the problems of low induction strength and slow response in transcription factor-dependent xylose transcriptional induction systems in the field of synthetic biology.

This invention provides a modified hemagglutinin (HA) protein for preparing a broad-spectrum vaccine against H9 avian influenza, a broad-spectrum vaccine based on the HA protein, a preparation method, and applications. The modified HA protein is obtained through the following strategy: consensus sequences are constructed as immunogenic backbones for the HA sequences of H9 avian influenza viruses at different epidemic periods; based on this, two types of functional mutations are directionally introduced: one type involves transplanting key epitope residues targeted by known broad-spectrum antibodies, and the other type involves neutralizing epitope residues predicted based on viral evolutionary patterns. The modified HA protein of this invention can maintain a highly similar overall fold and trimer interface to the wild type, can be efficiently expressed in eukaryotic systems, and can induce high levels of neutralizing antibodies with broad-spectrum cross-protective effects in target animals. It provides a core antigen candidate for the development of a new generation of H9 broad-spectrum vaccines and has broad application prospects.

The application relates to the technical field of DNA data storage, in particular to a DNA information encryption error correction method based on secondary structure fingerprint separation storage, which comprises the following steps: an information DNA coding stage, a structure signature generation stage, a signature DNA coding stage, an information DNA and signature DNA synthesis stage and a decoding and error correction stage; the information DNA coding stage is used for coding original data into information DNA segments; the structure signature generation stage is used for calculating structure characteristic parameters, generating compact structure signatures, and associating segment IDs with the compact structure signatures to form a signature data set; the signature DNA coding stage is used for coding the signature data set into signature DNA segments; the information DNA and signature DNA synthesis stage is used for respectively synthesizing the information DNA segments and the signature DNA segments and physically storing the information DNA segments and the signature DNA segments separately; and the decoding and error correction stage is used for verifying and correcting a consensus sequence based on the signature data set to recover the original data. The application stores the structure signature in an independent DNA molecule, thereby realizing physical layer encryption protection.

The application provides a mycobacterium tuberculosis small peptide display library and a construction method and application thereof, and the construction method comprises the following steps: S1, small peptide sequence information is obtained by intercepting according to mycobacterium tuberculosis proteome sequence information; S2, the amino acid sequence of the small peptide sequence information is converted into a codon sequence, sequence optimization is carried out, and after a consensus sequence is added, oligonucleotide sequence information is obtained; S3, an oligonucleotide physical object is synthesized in a large scale and in parallel by using a chemical method; S4, PCR amplification is carried out by taking the oligonucleotide physical object as a template, and after being digested by a restriction endonuclease, an inserted nucleic acid fragment is obtained; and S5, the inserted nucleic acid fragment is used to construct the small peptide display library by using a display system. The mycobacterium tuberculosis small peptide display library constructed by the application provides important tools and resources for systematically understanding mycobacterium tuberculosis immunological epitopes, vaccine development, new drug research and development and the like.