447 results about "Genome sequence analysis" patented technology

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 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.

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.

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 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.

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.

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 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%).

A method of determining the presence of a novel structural variation in a genome using long-read genome sequence fragments includes a process of aligning, filtering ranking and linking long-read sequence fragments against a reference genome. Presence of a novel structural variation is present in said genome can be determined when said linked alignment contains multiple linked fragments that are mapped to a single locus, referred to as a split-read.

The invention relates to a ultrahigh frequency antenna array partial discharge detection system comprising a partial discharging source and partial discharging sensors. The partial discharging source sends ultrahigh frequency signals and is arranged in a substation; the partial discharging sensors are arranged at the periphery of the partial discharging source, and the distances between each partial discharging sensor and the partial discharging source are different. Compared with the prior art, a principle of minimum optical path differences is utilized, transmit features of ultrahigh frequency electromagnetic signals produced by partial discharging source in the air are studied, influences on signal transmitting by positions of substation equipment are considered, and partial discharging positioning can be realized according to delay of signals reaching different detecting points; determination of the time of the first wave of the signals, method for acquiring the signal delay and realization of accurate positioning of discharging signals based on discharging signal delay sequence analysis and spatial analysis, by the methods of signal first wave value, power accumulation, time and space calculation and minimum power value, are studied.

The invention discloses an obtaining and an application of an oil-producing monoraphidium LB59, and relates to a screening and culturing technology of an oil-producing micro-alga. Through subjecting alga seeds separated from a field environment to 18SrDNA sequence analysis and morphological identification, the alga is determined to be a member of Monoraphidium, and the sequence is SEQ ID No.1. The oil-producing monoraphidium LB59 disclosed by the invention can tolerate high-concentrate sodium bicarbonate, is suitable for open type culture, is rich in grease, the grease content can reach 30.2% of dry cell weight under the condition that a growth and collection rate of 23.6g/m<2>d is held, and the fatty acid contains more than 20% of C-18 3-olefine acid and C-18 4-olefine acid.