468 results about "Genome sequence analysis" patented technology

A combinatorial method that uses statistics and DNA sequence analysis rapidly assesses the functional and structural importance of individual protein side chains to binding interactions. This general method, termed “shotgun scanning”, enables the rapid mapping of functional protein and peptide epitopes and is suitable for high throughput proteomics.

There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition.

Provided are methods for sequencing a nucleic acid that include fixing a template to a surface through a template localizing moiety and sequencing the nucleic acid with a sequencing enzyme, e.g. a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. The template localizing moiety can optionally anneal with the nucleic acid and / or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid fixed to a surface via a template localizing moiety, and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Compositions for sequencing reactions are provided. Also provided are sequencing systems comprising reaction regions in which or near which template localizing moieties are immobilized.

The present invention provides a sequence interrogation chemistry that combines the accuracy and haplotype integrity of long-read sequencing with improved methods of preparing genomic nucleic acids and analyzing sequence information generated from those nucleic acids. The present invention encompasses compositions comprising decorated nucleic acids stretched on substrates. The present invention further encompasses methods of making stretched decorated nucleic acids and methods of using decorated nucleic acids to obtain sequence information.

The present invention provides novel methods for reducing the complexity of preferably a genomic sample for further analysis such as direct DNA sequencing, resequencing or SNP calling. The methods use pre-selected immobilized oligonucleotide probes to capture target nucleic acid molecules from a sample containing denatured, fragmented (genomic) nucleic acids for reducing the genetic complexity of the original population of nucleic acid molecules.

Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.

A population of labeled probes is provided that utilize an encoding system in which both the intensity and specific characteristics of a signal molecule are utilized to reduce the number of signal molecules necessary to identify each member of the population of probes. In the population of labeled probes, each labeled probe includes a probe associated with a series of detectably distinguishable signal molecules. The number and type of signal molecules identifies the associated probe, and the number of probes in the population exceeds the number of unique signal molecules. The population of probes are used in methods of the invention and reaction mixtures of the invention, for identifying a target molecule and for sequencing a nucleic acid molecule, for example.

The invention discloses an epidemic situation predicting and early warning method of infectious diseases, particularly a network early warning system of relevant public health events of infectious diseases in countries, provinces, cities (regions) and districts (counties). The method comprises the steps of integrating adverse reaction information data which are collected by the server side, calculating and determining the early warning threshold of public health events according to the quantities of the symptoms of adverse reactions on the basis of the operation of a time sequence analysis statistic model and automatically carrying out early warning in real time at any time. The method comprises the following specific steps of: (1) integrating information from different channels; (2) executing a path I: analyzing tasks; and (3) executing a path II: predicting and early warning. Once the quantity of monitoring data meets the traditional basic requirements of a tome sequence analysis method for considering the periodicity, the seasonal nature, long term tend and the like of diseases, the conclusion having relative-high value can be obtained to play important roles of early finding epidemic situations, taking measures as soon as possible, preventing the spread of the epidemic situations and preliminarily establishing an epidemic situation monitoring and early warning system and a working mechanism of the province.

The present invention is generally directed to powerful and flexible methods and systems for consensus sequence determination from replicate biomolecule sequence data. It is an object of the present invention to improve the accuracy of consensus biomolecule sequence determination from replicate sequence data by providing methods for assimilating replicate sequence into a final consensus sequence more accurately than any one-pass sequence analysis system.

A usage model and the underlying technology used to provide sequence analysis as part of a relational database system. Included components include the semantic and syntactic integration of the sequence analysis with an existing query language, the storage methods for the sequence data, and the design of a multipart execution scheme that runs the sequence analysis as part of a potentially larger database query, especially using parallel execution techniques.

A foundation cloud measuring method combining infrared and lasers comprises the following steps that (1) atmosphere downward infrared radiation data are obtained through an uncooled infrared focal planar array sensor, zenith backward extinction coefficient profile data are obtained through a laser sensor, and the obtaining time of the atmosphere downward infrared radiation data is synchronous with the obtaining time of the zenith backward extinction coefficient profile data; (2) water vapor and aerosol radiation under cloud are estimated by combining the data, clear sky threshold values calculated through a radiation transmission pattern are used for conducting initial cloud detection, it is assumed that the cloud is a black body, and the cloud base height is obtained through inversion; (3) sequence analysis is conducted on infrared radiation images with high time resolution, the clear sky threshold values are combined to conduct further cloud detection, and the cloud cover is calculated; (4) proportionality coefficients between the cloud base height obtained through the infrared radiation inversion and the cloud base height obtained through laser measurement are fitted; (5) the cloud base height of a whole view field is corrected, and the typical cloud base heights of every ten minutes are obtained through calculation.

Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a desired property, or lacking nucleic acids having an undesired property. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations. In addition, such methods allow for analysis of pooled samples.

The invention relates to application and preparation of bacillus amyloliquefaciens subsp. plantarum and a bacterial agent thereof. An XH-9 bacterial strain is identified as bacillus amyloliquefaciens subsp. plantarum according to mycelial morphology, colony characteristics, physiological and biochemical indexes and 16S rDNA sequence analysis and is preserved in the China General Microbiological Culture Collection Center, and a preservation number is CGMCC NO.13151. The strain is high in antagonistic effect on pathogenic fungi such as fusarium oxysporum, bipolaris sorokiniana, fusarium pseudograminearum, colletotrichum gloeosporioides, botryosphaeria dothidea and alternaria alternata and is capable of generating heteroauxin and 1-aminocyclopropanecarboxylic acid (ACC) deaminase to stimulate plant growth and capable of degrading celluloses and can be stably colonized at rhizospheres of crops such as wheat, corn, peppers and the like. The bacterial agent prepared from the bacterial strain can be applied to prevention and treatment of root rot diseases or other soil-borne fungal diseases of crops such as wheat, corn, peppers and the like and has dual functions of disease prevention and growth promotion. The bacterial agent is simple in preparation process, short in fermentation period, low in cost and beneficial to industrial production and transport.

The invention discloses an industrialized gene synthesis method. The industrialized gene synthesis method comprises the following steps of (1) analyzing and optimizing a DNA sequence for synthesis to obtain a target DNA sequence; (2) designing an oligodeoxynucleotide chain for extension according to the target DNA sequence; (3) synthesizing and purifying the oligodeoxynucleotide chain; (4) splicing the oligodeoxynucleotide chain to form a DNA fragment; (5) cloning the DNA fragment to a vector to obtain a recombinant plasmid; (6) carrying out sequencing analysis of the recombinant plasmid; and(7) carrying out a quality validation process on the recombinant plasmid with a correct sequence. The industrialized gene synthesis method has the characteristics of high success rate, high throughput, high speed, low cost, simple design, wide application scope and standardized operation. Therefore, the industrialized gene synthesis method has feasibility of industrial scale popularization, and is beneficial for reduction of costs, shortening of a synthesis cycle and improvement of synthesis quality.

The present invention discloses methods for identifying and analysing microsatellite-associated polymorphisms between different DNA samples. Different DNA samples, e.g. from different individuals, are analysed using a PCR based on the combination of a RAMP-primer and an AFLP-primer and polymorphisms between the different DNA samples are identified. The polymorphisms thus identified may be isolated and further analysed by e.g. DNA sequence analysis both upstream and downstream from the microsatellite-associated polymorphism. These sequences may subsequently be used to devise and synthesise new means for analysis of the polymorphic locus, such as e.g. PCR-primer pairs or oligonucleotide probes.

The invention discloses acquisition and application of grease-producing monoraphidium LB50, and relates to screening and culture utilization technologies of the grease-producing monoraphidium. An algae species obtained by separating from field environment is subjected to 18S rDNA sequence analysis and morphological identification and is determined as a member of monoraphidium, and the sequence is shown as SEQ NO.1. The grease-producing monoraphidium LB50 is capable of bearing high-concentration sodium bicarbonate, is easy for open-type culture and is rich in grease; and when the growth and collection speed is kept at 22.2 g / m<2>*d, the grease content reaches 30.4% by dry weight of a cell, and aliphatic acid contained in grease contains octadecatrienoic acid and octadecatetraenoic acid which account 15% or more of aliphatic acid.

The invention provides a system anomaly detection method and system based on deep log sequence analysis. The method comprises the following steps: applying a sequence labeling model Bi-LSTM-CRF to logpath anomaly detection; applying normal distribution to log parameter anomaly detection, so that the BiLCN can automatically learn normal log modes including log execution paths and log event parameters, and log events deviating from a normal model can be accurately detected and marked as anomalies. Meanwhile, the system further comprises a log analyzer, a feature extractor and a log path flow model, the log path flow model is constructed through the detected log sequence, abnormal conditions are fed back to the user so that the user can diagnose the system in time, and experiments prove thatthe method has high accuracy and execution efficiency.

A method for producing a nucleic acid molecule from a template nucleic acid sequence and a linking unit attached to a primer, which method comprises a step of contacting the template nucleic acid sequence with a nucleic acid polymerase under conditions which allow the nucleic acid polymerase to produce the nucleic acid molecule from the primer based on the template nucleic acid sequence, wherein the linking unit is attached to a target site in the template nucleic acid sequence with a covalent linkage.

The invention relates to a novel beta glucosidase / xylosidase difunctional cellulose degradation enzyme RuGBGX2 as well as a coding gene and application thereof. The coding sequence of amino acid of the RuGBGX2 contains 18-755th sites of an SEQ ID NO 2 sequence. The RuGBGX2 is sourced from the rumen microorganism of yak from China, a novel coding gene of the beta glucosidase / xylosidase difunctional cellulose degradation enzyme RuGBGX2 is obtained by function screening and sequencing analysis on a rumen metagenome cosmid library and a subclone library. The beta glucosidase / xylosidase difunctional cellulose degradation enzyme provided by the invention can be widely applied to the degradation of cellulose and the fields such as cellulose biotransformation, chemical industry, spinning, foods, bioenergy, feed additives, medical industry and the like. By utilizing the difunctional enzyme RuGBGX2 to degrade wood fiber, the varieties of added enzymes can be reduced, and an enzymolysis process can be simplified.

The invention relates to a kit for identifying a Brucella S2 vaccine strain and a wild strain. The kit comprises a specific primer pair SEQ ID No.1 and SEQ ID No.2 for identifying the Brucella vaccine strain S2. Sequencing analysis is further performed on a PCR amplification product after the kit is used for distributing Brucella and other conventional bacterial strains through a PCR amplification-electrophoresis detection area, and the Brucella S2 vaccine strain in a clinic sample can be rapidly and effectively identified and diagnosed according to the sequencing result.

Apparatuses, compositions and processes for DNA barcode deconvolution are described herein. A DNA barcode may be used to provide a bead specific identifier, which may be detected in situ using hybridization strategies. The DNA barcode provides identification by sequencing analysis. The dual mode of detection may be used in a wide variety of applications to link positional information with assay information including but not limited to genetic analysis. Methods are described for generation of barcoded single cell sequencing libraries. Isolation of nucleic acids from a single cell within a microfluidic environment can provide the foundation for cell specific sequencing library preparation.

The invention relates to a multi-phosphopeptide-enriched casein hydrolyzate and a preparation method thereof. The method comprises the following steps of: with the casein as a raw material, suitably hydrolyzing by adopting a proteolytic enzyme, controlling a hydrolysis degree within 10 percent, heating with a boiling water bath for killing enzyme and separating out various polypeptide products from a reaction system by adopting an ultrafiltration membrane of 5 k Da; then, intercepting the product with a hyperfiltration membrane of 1 k Da and selectively precipitating phosphoeptide from the obtained intercepting liquid by adopting calcium-ethanol; dissolving the phosphoeptide with deionized water or a volatile salt solution, sampling on a strong cation exchange column and separating to obtain a plurality of phosphorylated peptides; acquiring a product by adopting spraying drying or freezing drying; and finally, carrying out the sequence analysis on the obtained phosphoeptide by adopting LC / MS (Coupled HPLC-Mass Spectrometry). The invention can selectively acquire the phosphoeptide with higher activity, has favorable application prospects in the field of food biotechnology and provides a favorable research sample for researching phosphoproteomics.

The invention discloses a monascus strain and application of the monascus strain in preparing functional monascus. The Monascus sp. strain MS-1 provided by the invention is conserved in China Center for Type Culture Collection on June 26, 2013 with the conservation number of CCTCC M2013295. The strain is identified as M.pilosus through morphology and an ITS sequence analysis method. The Monascus sp. strain MS-1 does not contain ctnA, ctnE, ctnR or pksCT genes related to the synthesis of citrinin in the genome and does not have the citrinin synthesizing capability. The invention further provides a method for producing the functional monascus rich in monacolin K but containing no citrinin. The method comprises the following steps: (1) bringing the Monascus sp. strain MS-1 into a seed medium for enrichment culture to obtain a seed solution; (2) taking the seed solution into a fermentation medium for solid fermentation, wherein a temperature change culture method is adopted, the seed solution is cultured for three days at 30 DEG C and then cultured for 11 days at 25 DEG C; and (3) drying the fermentation product at 55 DEG C to obtain the functional monascus. The content of the monacolin K in the functional monascus is high, and the detection shows no citrinin exists.

The invention discloses a technology for constructing an intelligent prediction model of a protein secondary structure, and the model is integrated by a structural model with multi-layer recursive and stepwise refinement. The model CPM fuses an inventive KAAPRO method, a novel homologous analysis method, an improved SVM method and the like. The CPM breaks through the technical route of the traditional single physical and chemical attribute analysis or a single structural sequence analysis, and adopts a preferred route by combining the structural sequence analysis and the physical and chemical attribute analysis to ensure the optimization of the whole model good prediction precision and better universality. The CPM is mined by a high-starting-point alpha / beta base and goes through domain knowledge and background knowledge; and the CPM can better predict the secondary structure of a meta-alpha / beta protein and has the highest precision of 86% (the highest precision of the similar type is 81%).

This invention relates to the special short peptide of hepatoma cell internalization and its screen and identification in vitro, belonging to the technology of tumor cell peptides screening and identification. It takes hepatoma cell BEL-7404 as the screening target cell, displays the random 12-peptide library for bacteria invader to conduct affinity panning. Through three times of screen, it randomly selects twenty negative colonies for amplification and sequence, to deduct the amino acid sequence of random peptide. Through cell ELISA, immunofluorescence, flow cytometry and other method, it further identifies the combination and internalization of bacteria invader clones and hepatoma cells. From sequencing and sequence analysis of the positive clones, four obtained different sequences have good combination with hepatoma cells, and the screened monoclone can internalize cells.