1206 results about "Sequence analysis" patented technology

Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.

Presented herein are methods and compositions for multiplexed single cell gene expression analysis. Some methods and compositions include the use of droplets and/or beads bearing unique barcodes such as unique molecular barcodes (UMI).

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.

The present invention provides a method, device and a computer program for haplotyping single cells, such that a sample taken from a pregnant female, without directly sampling the fetus, provides the ability to non-invasively determine the fetal genome. The method can be performed by determining the parental and inherited haplotypes, or can be performed merely on the basis of the mother's genetic information, obtained preferably in a blood or serum sample. The novel device allows for sequence analysis of single chromosomes from a single cell, preferably by partitioning single chromosomes from a metaphase cell into long, thin channels where a sequence analysis can be performed.

The invention is directed to methods of generating sequence profiles of populations of nucleic acids, whose member nucleic acids contain regions of high variability, such as populations of nucleic acids encoding T cell receptors or B cell receptors. In one aspect, the invention provides pluralities of sets of primers for generating nested sets of templates from nucleic acids in such populations, thereby insuring the production of at least one template from which sequence reads are generated, despite such variability, or dispite limited lenghs or quality of sequence reads. In another aspect, members of such populations are bidirectionally sequenced so that further sequence information is obtained by analyzing overlapping sequence reads in the zones of highest variability.

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.

The invention discloses a method for identifying the video action based on trajectory sequence analysis and rule induction, which solves the problems of large labor intensity. The method of the invention divides a complete trajectory in a scene into a plurality of trajectory section with basic meaning, and obtains a plurality of basic movement modes as atomic events through the trajectory clustering; meanwhile, a hidden Markov model is utilized for establishing a model to obtain the event rule contained in the trajectory sequence by inducting the algorithm based on the minimum description length and based on the event rule, an expanded grammar analyzer is used for identifying an interested event. The invention provides a complete video action identification frame and also a multi-layer rule induction strategy by taking the space-time attribute, which significantly improves the effectiveness of the rule learning and promotes the application of the pattern recognition in the identification of the video action. The method of the invention can be applied to the intelligent video surveillance and automatic analysis of movements of automobiles or pedestrians under the current monitored scene so as to lead a computer to assist people or substitute people to complete monitor tasks.

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 relates to a method which can prevent handheld camera equipment from shaking when shooting. The method comprises the following steps of: judging a normal shutter speed needed by brightness on a current scene whether have exceeded a safe shutter speed of the handheld camera equipment or not; if no, directly releasing a shutter for shooting; if so, analyzing high-speed image sequences based on a preview mode to confirm size of the current handheld camera equipment when the equipment is shaking; confirming current shaking whether is larger than a set threshold value according to a preset threshold value range, if the current shaking is smaller than the set threshold value, so a user can be allowed to press down the shutter for shooting; if the shaking continuously becomes larger within a certain time, a condition for shutter releasing is not satisfied, so exposure parameters can be automatically adjusted, namely, gain can be automatically increased, meanwhile, exposure time is reduced, moreover, the threshold value used for judging degree of shaking is correspondingly enlarged, so that the shooting is easier to be reached within an allowable shaking range.

A temperature compensation method for denoising a fiber-optic gyroscope on the basis of time series analysis comprises four steps of: step 1, designing an experimental scheme, performing fixed point low and high temperature testing experiment on the fiber-optic gyroscope, and utilizing acquisition software for data acquisition; step 2, performing time series analysis on the zero offset data of the gyroscope, and establishing the mathematical model of the random error of the fiber-optic gyroscope; step 3, adopting a kalman filtering algorithm to filter random noise in the zero offset data of the fiber-optic gyroscope; and step 4, utilizing the data which is de-noised by the kalman filtering to identify the model structure of the temperature shift error of the fiber-optic gyroscope, and calculating the parameters of the identified model. The method establishes the multinomial model of the static temperature shift error of the fiber-optic gyroscope through time series analysis, kalman filtering denoising treatment and identification of the temperature shift error model structure and parameters. The method completely meets the real-time compensation requirement on the project, and has a better practicable value and a wide application prospect in the technical field of aerospace navigation.

A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

A method and system for quantifying the relative abundance of gene transcripts in a biological sample. One embodiment of the method generates high-throughput sequence-specific analysis of multiple RNAs or their corresponding cDNAs (gene transcript imaging analysis). Another embodiment of the method produces a gene transcript imaging analysis by the use of high-throughput CDNA sequence analysis. In addition, the gene transcript imaging can be used to detect or diagnose a particular biological state, disease, or condition which is correlated to the relative abundance of gene transcripts in a given cell or population of cells. The invention provides a method for comparing the gene transcript image analysis from two or more different biological samples in order to distinguish between the two samples and identify one or more genes which are differentially expressed between the two samples.

An isolated nucleic acid, a recombinant protein encoded thereby and uses thereof. The isolated nucleic acid including (a) a polynucleotide at least 60% identical to SEQ ID NOs:1, 3, 5 or portions thereof as determined using the Bestfit procedure of the DNA sequence analysis software package developed by the Genetic Computer Group (GCG) at the university of Wisconsin (gap creation penalty-50, gap extension penalty-3); (b) a polynucleotide encoding a polypeptide being at least 60 homologous with SEQ ID NOs:2, 4, 6 or portions thereof as determined using the Bestfit procedure of the DNA sequence analysis software package developed by the Genetic Computer Group (GCG) at the university of Wisconsin (gap creation penalty-50, gap extension penalty-3); or (c) a polynucleotide hybridizable with SEQ ID NOs:1, 3, 5 or portions thereof at 68° C. in 6xSSC, 1% SDS, 5xDenharts, 10% dextran sulfate, 100 mug/ml salmon sperm DNA, and 32p labeled probe and wash at 68° C. with 3xSSC and 0.1% SDS.

A dual-stage regular expression pattern matching method and system is proposed, which is designed for integration to a data processing system, such as a computer platform, a firewall, a network intrusion detention system (NIDS), or a DNA sequence analysis system, for checking whether an input code sequence (such as a network data packet) is matched to specific patterns predefined by regular expressions. The proposed system and method includes a first-stage comparison procedure for comparison of the prefix string of each input code sequence and a second-stage comparison procedure for comparison of the postfix string of the same input code sequence. This feature can be used for processing code sequences having a special pattern without producing an enormous amount of state data that would cause the problem of insufficient memory during operation.

An image selection method includes receiving a collection of images and optionally, filtering the collection of images. The filtering may include removing images that are near-duplicates of other images in the collection. A plurality of features is extracted from each of the images in the optionally-filtered collection. The optionally-filtered collection of images is considered as a time-ordered sequence of images and is segmented to form a sequence of segments. Each segment includes at least one of the images. The segmenting of the sequence of images is based on the extracted features and positions of the images in the sequence of images. Images from the segments are selected to form a sub-collection of the images.

The invention discloses a method for evaluating the reliability of a stepping stress quickened degradation experiment based on a time sequence. The method utilizes a correlation coefficient stationary sequence analytical method to describe non-equidistant stochastic information in stepping stress quickened degradation experiment data, establishes a regressive-non-equidistant autoregression degradation model on the basis of obtaining the respective advantages of a deterministic regression model and a stochastic correlation coefficient stationary sequence autoregression model, combines a grey theory to predict a product degradation trend and forms a function and a curve for predicting the life and evaluating the reliability of the stepping stress quickened degradation experiment based on the time sequence. The method obviously decreases the sample quantity of a product and shortens the time of the degradation experiment, thereby saving a large amount of expenses and resources, enhancing the fitting accuracy of the degradation model and enhancing the reliability of a reliability evaluating result.