212 results about "Sequenceome" patented technology

This invention includes methods for identifying nucleic acids in a sample of nucleic acids by observing sequence sets present in the nucleic acids of the sample and then identifying those sequences in a nucleic acid sequence database having the sequence sets observed. In a preferred embodiment, a sequence set consists of two primary subsequences and an additional subsequence having determined mutual relationships. The methods include those for observing the sequence sets and those for performing sequence database searches. This invention also includes devices for recognizing in parallel the additional subsequences in a sample of as well as methods for the use of these devices. In a preferred embodiment, the devices include probes bound to a planar surface that recognize additional subsequence by hybridization, and the methods of use include features to improve the specificity and reproducibility of this hybridization.

A method and system for conducting sequence searches in a sequence database wherein in one embodiment, the method includes: combining a plurality of query sequences into a combined query sequence; determining a plurality of subdivisions of the sequence database; performing a plurality of searches, wherein each search includes a comparison of the combined query sequence against one of the plurality of subdivisions of the database to produce a plurality of word matches; extending the length of the plurality of word matches to produce a plurality of High-scoring Segment Pairs, combining the plurality of High-scoring Segment Pairs; and producing a plurality of reports, each report representing the highest scoring matches for one of the plurality of query sequences.

This invention includes methods for identifying nucleic acids in a sample of nucleic acids by observing sequence sets present in the nucleic acids of the sample and then identifying those sequences in a nucleic acid sequence database having the sequence sets observed. In a preferred embodiment, a sequence set consists of two primary subsequences and an additional subsequence having determined mutual relationships. The methods include those for observing the sequence sets and those for performing sequence database searches. This invention also includes devices for recognizing in parallel the additional subsequences in a sample of as well as methods for the use of these devices. In a preferred embodiment, the devices include probes bound to a planar surface that recognize additional subsequence by hybridization, and the methods of use include features to improve the specificity and reproducibility of this hybridization.

A method for detecting one or more HLA sequence types is described that comprises the steps of: amplifying a plurality of first amplicons from a double stranded nucleic acid sample, wherein the first amplicons are amplified with a plurality of pairs of nucleic acid primers that define exons 2 and 3 of both strands of HLA loci from the group consisting of HLA-A, HLA-B, and HLA-C; amplifying the first amplicons to produce a plurality of populations of second amplicons, wherein each population of second amplicons is clonally amplified from one of the first amplicons; sequencing the plurality of populations of second amplicons to generate a nucleic acid sequence composition for each of the plurality of second amplicons; and detecting variation in the sequence composition from one or more of the second amplicons for one or more of the HLA loci.

A modified pectin consists essentially of neutral sugar sequences with a low degree of branching capable of preventing tumor cell migration and cell to cell and cell to substratum adhesion.

The invention relates to methods for clustering gene and protein sequences. In particular, it involves generation of networks of sequences where the interconnections are based upon a measure of similarity. The invention also provides methods of optimizing and improving the networks by re-wiring of the network based upon overlap of the nearest neighbors of given pairs of nodes. The invention further provides methods of identifying clusters of sequences within the networks and the optimized networks based upon the topology of the network. The clusters identified represent groups of sequences that are related by function and / or evolution. The invention has particular applicability in annotation of sequences in databases and identification of functional homologs which can be very useful for novel therapeutic and diagnostic targets based upon such targets belonging to a cluster or family that contains a known sequence such as a diagnostic sequence, antigen or other therapeutic target.

The present invention provides compositions and methods for the detection and characterization of HPV sequences. More particularly, the present invention provides compositions, methods and kits for using invasive cleavage structure assays (e.g. the INVADER assay) to screen nucleic acid samples, e.g., from patients, for the presence of any one of a collection of HPV sequences. The present invention also provides compositions, methods and kits for screening sets of HPV sequences in a single reaction container.

The present invention provides a polynucleotide which consists of a partial sequence of a polynucleotide encoding the amino acid sequence as shown in SEQ ID NO: 2, wherein the former polynucleotide encodes a polypeptide consisting of a partial amino acid sequence of SEQ ID NO: 2 whose N-terminus starts between positions 564 and 621 of SEQ ID NO: 2.

The invention provides a polypeptide chip, which comprises a substrate and n polypeptides distributed on the substrate in an array, each polypeptide sequence has 10-20 amino acids, a group consistingof sequences of first to nth polypeptides covers at least 95% of a viral protein sequence, the adjacent polypeptides have an overlap of 3-8 amino acids, and n is 810-1370. According to the method, proteomics and system biology strategies are adopted, all coded protein sequences of COVID-19 are extracted from NCBI data, an SARS-CoV-2 virus proteome polypeptide chip is designed and prepared, and panoramic scanning of all SARS-CoV-2 virus antibodies in blood of a novel pneumonia virus infected patient is achieved.

The invention discloses a distribution method of a signature sequence or a signature sequence group on an E-HICH, comprising the following steps of determining a value of each parameter needed when distributing the signature sequence or the signature sequence group to each user equipment UE which shares a same enhanced physical uplink channel (E-PUCH); and distributing corresponding signature sequence or signature sequence group to each UE which shares the same E-PUCH according to the value of each parameter. By the method, different signature sequences or different signature sequence groupsare distributed to each UE sharing the same E-PUCH, and therefore, NODEB can respectively feed back control information of the E-PUCH of each UE to each UE sharing the same E-PUCH by distributing thesignature sequence or the signature sequence group to each UE.

The invention discloses a combined primer for the amplification and typing of human papilloma virogenes. The combined primer is divided into a combined forward primer and a combined reverse primer; the combined forward primer is composed of three parts, namely a joint part P2 sequence, a tag sequence and a forward primer sequence in order; the combined reverse primer is composed of a reverse primer sequence and a joint part P1 sequence in order. The invention also discloses a kit for the amplification and typing of the human papilloma virogenes. The invention also discloses the applications of the combined primer and the kit. The combined primer has real flux, and is low in cost and capable of accurately typing HPV. The type of HPV can be accurately determined by using a plurality of primers (6 forward primers and 5 reverse primers) for amplification and comparing the sequence information of the amplification product with an HPV database; as a result, a basis is provided for clinical diagnosis and treatment scheme selection.

The invention provides a polynucleotide for identifying male and female ginkgo strains. The polynucleotide comprises or consists of: 1) a nucleotide sequence shown as SEQ ID NO: 5; or 2) a complement,degenerate or homologous sequence of the sequence shown as SEQ ID NO: 5; or 3) a polynucleotide which hybridizes to the nucleotide sequence shown in SEQ ID NO: 5 under stringent conditions or a complement thereof; 4) a coding sequence of any of the sequences 1) to 3); or 5) a nucleotide sequence identical to a nucleotide of 10 bp or more in any of the sequences of sequences 1) to 4). The polynucleotide provided by the present invention is unique among male ginkgo plants, uses the same to identify male and female plants of ginkgo, has the advantages of stable and accurate results, good reproducibility and rapid detection, and provides a basis for the identification of male and female ginkgo by molecular markers.

The invention discloses a primer set and method for identifying variety authentication and seed purity of tomatoes. Sequences of 48 pairs of primers of the primer set for identifying variety authentication of tomatoes and purity of seeds is successively as shown in sequences 1-96 in a sequence table, a sequence 2n and a sequence 2n-1 form a primer pair, and n is a natural number in 1-24. The method for identifying variety authentication and seed purity of tomatoes comprises the following steps: carrying out PCR amplification on DNA of tomatoes to be detected by using the primer set; and determining variety authentication and seed purity of the tomatoes to be detected according to difference of PCR products of the tomatoes to be detected. Experiments prove that the primer set not only can be used for identifying the variety authentication of the tomatoes, but also can be used for identifying the seed purity of the tomatoes, and has the advantages that the accuracy is high, results are stable, the primer set is not affected by environment conditions and development stages, statistics is simple and convenient and the like.

The invention discloses the use of variovoraxboronicumulans CGMCC 4969 in bioconversion of 3-cyanopyridine for forming nicotinamide. The nitrile hydratase gene cluster produced by the strain consists of a DNA sequence represented by SEQ ID No.1 in a sequence table; the DNA consisting of the sequence represented by SEQ ID No.1 is recombined onto a pET28a plasmid and can be induced to express in EscherichiacoliBL21(DE3) strain; and the Escherichia coli cells containing expressed proteins and cell extracting solution can convert 3-cyanopyridine into nicotinamide.

An improved method is provided for solving waveform description, matching and comparison problems using attractor-based processes to extract identity tokens that indicate sequence and subsequence symbol content and order of the waveform or waveform segments. The waveform is described with a suitable alphabet to extract the ontology of the waveform, and syntactical rules are applied to direct pattern extraction using the alphabet. The patterns are extracted in a hierarchical, embedded manner according the global or local maximia and minimia so that the resulting statements are compatible with analysis in catastrophe theory. The attractor processes map the resulting waveform sequence from its original sequence representation space (OSRS) into a hierarchical multidimensional attractor space (HMAS). The HMAS can be configured to represent equivalent symbol distributions within two symbol sequences or perform exact symbol sequence matching. The mapping process results in each sequence being drawn to an attractor in the HMAS. Each attractor within the HMAS forms a unique token for a group of sequences with no overlap between the sequence groups represented by different attractors. The size of the sequence groups represented by a given attractor can be reduced from approximately half of all possible sequences to a much smaller subset of possible sequences. The mapping process is repeated for a given sequence so that tokens are created for the whole sequence and a series of subsequences created by repeatedly removing a symbol or group of symbols from the one end of sequence and then repeating the process from the other end. The resulting string of tokens represents the exact identity of the whole sequence and all its subsequences ordered from each end.

The invention discloses a test strip RPA primer for detecting Ditylenchus destructor. The primer is composed of nucleotide sequences as shown in SEQ ID No:1 and SEQ ID No:2. The invention further discloses a combination of the primer and a probe, and the probe is composed of a sequence as shown in SEQ ID No:3. In addition, the invention discloses a detection kit comprising the primer and probe combination. The combination of the test strip RPA primer and the probe has the advantages of strong detection specificity for the Ditylenchus destructor, high sensitivity, low requirements on equipmentand personnel quality, simplicity in operation, high detection speed and low cost, and is suitable for port quarantine and basic level on-site detection.

The invention relates to a CRISPR (clustered regularly interspaced short palindromic repeat) detection primer group for mycoplasma pneumoniae and an application of the CRISPR detection primer group, and belongs to the technical field of gene detection of a CRISPR technology. The primer group comprises an amplification primer pair and crRNA (CRISPR-derived ribonucleic acid), wherein the amplification primer pair is used for amplifying a sequence shown as SEQ ID NO. (sequence identifier number) 1 of the mycoplasma pneumoniae; crRNA comprises an anchor sequence and a guide sequence; the anchor sequence specifically identifies a Cas protein; and the guide sequence is matched with a target sequence segment in the sequence of SEQ ID NO. 1. The primer group detects the mycoplasma pneumoniae through the CRISPR technology; the detection time of the mycoplasma pneumoniae is shortened; and the detection can be accomplished within 60min. A specific sequence combination obtained by screening acts as the primer group for detection, the primer group has the advantages of high sensitivity and strong specificity, and a limit of detection of the primer group can reach 30 copies. The primer group isused for the CRISPR detection of the mycoplasma pneumoniae, is independent of a complicated variable temperature amplification instrument such as a qPCR (quantitative polymerase chain reaction) instrument, and a CRISPR-Cas technology has wide application prospects in instant diagnosis of the mycoplasma pneumoniae.

The invention discloses a small interfering RNA (siRNA) inhibiting expression of a myostatin (MSTN) gene in chicken and application thereof. The invention provides an siRNA which acts on the MSTN gene, wherein the siRNA is a) a double-stranded RNA composed of the sequence 1 and the sequence 2 in a sequence table, b) a double-stranded RNA composed of the sequence 3 and the sequence 4 in the sequence table or c) a double-stranded RNA composed of the sequence 5 and the sequence 6 in the sequence table. The invention obtains the siRNA effectively inhibiting expression of the MSTN gene in chicken,real-time quantitative polymerase chain reaction (PCR) verifies that the siRNA effectively reduces expression of MSTN in molecular biology, and chicken with skeletal muscles obviously increased are successively obtained through microinjection test in embryology. The above results show that the siRNA provided by the invention can be used for breeding chicken, thus improving the meat yields of broilers, especially high quality chicken.

The invention discloses whole genome re-sequencing analysis and a method for the whole genome re-sequencing analysis. The method for whole genome re-sequencing analysis comprises the following steps of: acquiring a plurality of sequencing sequences obtained by identifying a DNA sequence of a sample to be detected, dividing the plurality of sequencing sequences into a plurality of sequencing sequence groups, based on each sequencing sequence group, executing the following operations in parallel: sequentially or parallelly comparing each sequencing sequence in the sequencing sequence group witha reference genome, and determining a corresponding position of each sequencing sequence on the reference genome and a corresponding chromosome number, and according to the corresponding position of each sequencing sequence on the reference genome and the corresponding chromosome number, conducting sequencing and duplicate removal on each sequencing sequence, and generating a sequencing sequence library corresponding to each chromosome.

An object of the present invention is to discover an endogenous wheat sequence satisfying the conditions of: a) it is universally present in varieties of wheat, b) the amount present (detected amount) is not affected by the wheat variety, c) even if other grains are present, only wheat can be detected without cross-reactivity, and d) it is amplified quantitatively by the PCR reaction. A further object of the present invention is to provide a method of accurately detecting and quantitating endogenous wheat DNA in a test sample by the polymerase chain reaction. The present invention provides a method of detecting or quantitating endogenous wheat DNA in a test sample by the polymerase chain reaction, the method comprising: a step of using a nucleic acid molecule in the test sample or a nucleic acid molecule extracted from the test sample as a template to amplify the nucleic acid molecule of a region consisting of the nucleotide sequence identified as SEQ ID NO: 2 or a partial sequence thereof with a primer pair capable of amplifying that region; and a step of detecting or quantitating the amplified nucleic acid molecule.

The invention discloses Variovorax boronicumulans CGMCC 4969 capable of biologically degrading acrylamide. The amidase gene of the Variovorax boronicumulans CGMCC 4969 is composed of a DNA sequence represented by SEQ ID No:1 in a sequence table; DNA fragments composed of the sequence represented by the SEQ ID No:1 are inserted into an Escherichia coli expression vector pET28a plasmid to obtain a recombinant pET28a-amidase; and the recombinant pET28a-amidase is transformed into an Escherichia coli Rosetta strain, the amidase is expressed through induction, and Escherichia coli cells containing expression proteins can degrade acrylamide.

The invention relates to a composition for detecting 23 respiratory pathogens. The composition comprises a primer composition consisting of the sequences shown by SEQ ID NO. 1-SEQ ID NO. 48 and a probe composition consisting of the sequences shown by SEQ ID NO. 49-SEQ ID NO. 72. The invention also relates to a kit for detecting 23 respiratory pathogens and a detection method of the kit. The kit comprises a first reaction solution, a second reaction solution, a first hybridization solution and a second hybridization solution containing the primers and probes respectively; the kit also comprises a mixed enzyme, a streptavidin-phycoerythrin solution, a negative reference, a positive reference and an interior label. The kit and the detection method provided by the invention integrate the functions of RT-PCR, full-automatic liquid-phase chip hybridization detection, data analysis and the like, and also have the advantages of high throughput, multiple detection target spots, high degree of automation, easiness in operation, short time consumption among the inventions of the same kind of liquid-phase chip technologies, etc.; moreover, the kit and the detection method provide important information for addressing the respiratory tract infection epidemic in time, and are of great significance to the prevention and control of respiratory pathogens.

The invention discloses a protein for controlling rice lesion mimic characters. The protein is formed by an amino acid sequence as shown by SEQ ID NO. 2 in a sequence table or a derivative sequence thereof. The invention further discloses a gene for encoding the protein. The gene is formed by a nucleotide sequence as show by SEQ ID NO. 1 in the sequence table. The lesion mimic gene provided by the invention has a good effect on resistance to rice bacterial blight, can be used for improving the bacterial blight resistance of nonglutinous rice, and provides a new way for breeding the nonglutinous rice capable of resisting bacterial blight; secondly, a new gene knockout technology is applied, a lesion mimic material under the background of japonica rice is acquired successfully, and a new method for utilizing the gene to culture japonica rice variety capable of resisting bacterial blight is provided. In addition, the gene provided by the invention is controlled by a single recessive gene, a transgene or filial generation can be simply identified and selected, and the convenience in application is realized.

The invention discloses a siRNA capable of restraining chicken myostatin (MSTN) gene expression and application of the siRNA; small interfering RNA (ribonucleic acid) acted on myostatin gene is provided by the invention and is a) or b) or c) as follows: a) double-stranded RNA composed of a sequence 1 of a sequence table and a sequence 2 of the sequence table; b) double-stranded RNA composed of a sequence 3 and a sequence 4 of the sequence table; and c) double-stranded RNA composed of a sequence 5 and a sequence 6 of the sequence table; according to the invention, the small interfering RNA effectively capable of restraining chicken MSTN gene expression is obtained and is proved to effectively reduce expression of MSTN through real-time fluorescent quantitative PCR (polymerase chain reaction) on molecular biology; chicks with obviously enlarged skeletal muscle is successfully acquired through a micro-injection test on embryology; above-mentioned results show that the small interfering RNA provided by the invention can be used for breeding the chicks, so that chicken yield of the chicks specifically high-quality chicks is increased.

The invention discloses a DNA fragment and an application thereof in preparation of an H5N1-subtype flu Guassia luciferase reporter virus. The nucleotide sequence of the DNA fragment is composed of following sequences in a successive series manner: an H5N1-subtype flu virus NA segment 3'-terminal noncoded region coding gene sequence, an H5N1-subtype flu virus NA gene encoded region coding sequence, a PTV-1 virus 2A peptide encoded gene sequence, a Gaussia luciferase encoded gene sequence, a H5N1-subtype flu virus NA segment 5'-terminal packaged signal encoded gene sequence, and a H5N1-subtype flu virus NA segment 5'-terminal noncoded region coding sequence. By means of the recombined H5N1-subtype flu reporter virus prepared with the DNA fragments, quantitative detection on viruses in a sample can be objectively carried out quickly and accurately through activity of luciferase in cellular supernatant or animal serum. The H5N1-subtype flu Guassia luciferase reporter virus can not only save time but also improve accuracy and reliability of a detection result, thereby providing a new convenient and effective tool for drug screening and vaccine assessment of anti-H5N1-subtype flu virus drugs.