3068 results about "Sequencing data" patented technology

An embodiment of an identifier element for identifying an origin of a template nucleic acid molecule is described that comprises a nucleic acid element comprising a sequence composition that enables detection of an introduced error in sequence data generated from the nucleic acid element and correction of the introduced error, where the nucleic acid element is constructed to couple with the end of a template nucleic acid molecule and identifies an origin of the template nucleic acid molecule.

Methods of enzymatic nucleic acid sequencing are provided in which solid-phase capturable chain terminators are employed. In the subject methods, sequencing fragments are generated, where the fragments comprise capturable chain terminators. The fragments are then captured on a solid phase and separated from the remaining components of the sequencing reaction. The fragments are then released from the solid phase, size separated and detected to yield sequencing data from which the sequence of the nucleic acid is determined.

The present invention is directed to methods and compositions for long fragment read sequencing. The present invention encompasses methods and compositions for preparing long fragments of genomic DNA, for processing genomic DNA for long fragment read sequencing methods, as well as software and algorithms for processing and analyzing sequence data.

Music piece sequence data are composed of a plurality of event data which include performance event data and user event data designed for linking a voice to progression of a music piece. A plurality of voice data files are stored in a memory separately from the music piece sequence data. In music piece reproduction, the individual event data of the music piece sequence data are sequentially read out, and a tone signal is generated in response to each readout of the performance event data. In the meantime, a voice reproduction instruction is output in response to each readout of the user event data. In accordance with the voice reproduction instruction, a voice data file is selected from among the voice data files stored in the memory, and a voice signal is generated on the basis of each read-out voice data.

A system or method consistent with an embodiment of the present invention is useful in analyzing large volumes of different types of data, such as textual data, numeric data, categorical data, or sequential string data, for use in identifying relationships among the data types or different operations that have been performed on the data. A system or method consistent with the present invention determines and displays the relative content and context of related information and is operative to aid in identifying relationships among disparate data types. Various data types, such as numerical data, protein and DNA sequence data, categorical information, and textual information, such as annotations associated with the numerical data or research papers may be correlated for visual analysis. A variety of user-selectable views may be correlated for user interaction to identify relationships that exist among the different types of data or various operations performed on the data.Furthermore, the user may explore the information contained in sets of records and their associated attributes through the use of interactive 2-D line charts and interactive summary miniplots.

The present disclosure provides a novel approach for shifting or distributing various information (e.g., protocols, analysis methods, sample preparation data, sequencing data, etc.) to a cloud-based network. For example, the techniques relate to a cloud computing environment configured to receive this information from one or more individual sample preparation devices, sequencing devices, and / or computing systems. In turn, the cloud computing environment may generate information for use in the cloud computing environment and / or to provide the generated information to the devices to guide a genomic analysis workflow. Further, the cloud computing environment may be used to facilitate the sharing of sample preparation protocols for use with generic sample preparation cartridges and / or monitoring the popularity of the sample preparation protocols.

Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

A system and method for performing biological sequence similarity searching is disclosed. This includes a programmable logic device configured to include a pipeline that comprises a matching stage, the matching stage being configured to receive a data stream comprising a plurality of possible matches between a plurality of biological sequence data strings and a plurality of substrings of a query string. The pipeline may further include a ungapped extension prefilter stage located downstream from the matching stage, the prefilter stage being configured to shift through pattern matches between the biological sequence data strings and the plurality of substrings of a query string and provide a score so that only pattern matches that exceed a user defined score will pass downstream from the prefilter stage. The matching stage may include at least one Bloom filter.

A data flow egress scheduler and shaper provides multiple levels of scheduling for data packets exiting communications devices. A classifier separates data from multiple sources by data flow and by priority within a data flow. An output controller requests a data packet for transmission and the scheduler selects a next available highest priority packet from a next in sequence data flow or from a management data queue. The shaper can control the rates of classes of service to be scheduled by the device. The scheduler typically comprises three levels of scheduling. Large numbers of output ports can be implemented in a single device by a virtual scheduler that services each data flow, output port and data source as a shared component, maintain context for groups of schedulers and data flows.

The present invention relates to methods for evaluating and / or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and / or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and / or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and / or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.

The present invention discloses a rice whole genome SNP chip and an application thereof. A method for preparing the chip comprises: (1) obtaining a first class of probes on a chip, wherein sequencing is performed to obtain a parental genome sequence, resequencing data of other rice varieties in a public database are combined, a Nipponbare genome is adopted as a reference sequence, a MAQ software is adopted to match and analyze all the sequencing data, and finally a SNP marker is screened; (2) obtaining a second class of probes on the chip, wherein a rice function gene is obtained from the public database, sequence difference reflecting gene function is searched, and a SNP / INDEL probe is designed according to the sequence difference; (3) adopting an infinium chip manufacturing technology to produce a SNP chip; and (4) testing accuracy and application efficiency of the chip. The chip of the present invention can be applicable for rice germplasm resource molecule marker fingerprint analysis, seed authenticity detection, filial generation genotyping, and other related researches.

Methods, processes, and particularly computer implemented processes and computer program products are provided for use in the analysis of genetic sequence data. The processes and products are employed in the assembly of shorter nucleic acid sequence data into longer linked and preferably contiguous genetic constructs, including large contigs, chromosomes and whole genomes.

Systems and methods for analyzing genetic sequence data involve: (a) obtaining, by a computer system, genetic sequencing data pertaining to a subject; (b) splitting the genetic sequencing data into a plurality of segments; (c) processing the genetic sequencing data such that intra-segment reads, read pairs with both mates mapped to the same data set, are saved to a respective plurality of individual binary alignment map (BAM) files corresponding to that respective segment; (d) processing the genetic sequencing data such that inter-segment reads, read pairs with both mates mapped to different segments, are saved into at least a second BAM file; and (e) processing at least the first plurality of BAM files along parallel processing paths. The plurality of segments may correspond to any given number of genomic subregions and may be selected based upon the number of processing cores used in the parallel processing.

Disclosed herein are methods of determining the sequence and / or positions of modified bases in a nucleic acid sample present in a circular molecule with a nucleic acid insert of known sequence comprising obtaining sequence data of at least two insert-sample units. In some embodiments, the methods comprise obtaining sequence data using circular pair-locked molecules. In some embodiments, the methods comprise calculating scores of sequences of the nucleic acid inserts by comparing the sequences to the known sequence of the nucleic acid insert, and accepting or rejecting repeats of the sequence of the nucleic acid sample according to the scores of one or both of the sequences of the inserts immediately upstream or downstream of the repeats of the sequence of the nucleic acid sample.

The present disclosure provides compositions and methods for accurately detecting mutations by uniquely tagging double stranded nucleic acid molecules with dual cyphers such that sequence data obtained from a sense strand can be linked to sequence data obtained from an anti-sense strand when sequenced, for example, by massively parallel sequencing methods.

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.

Systems and methods for determining structural variation and phasing using variant call data obtained from nucleic acid of a biological sample are provided. Sequence reads are obtained, each comprising a portion corresponding to a subset of the test nucleic acid and a portion encoding a barcode independent of the sequencing data. Bin information is obtained. Each bin represents a different portion of the sample nucleic acid. Each bin corresponds to a set of sequence reads in a plurality of sets of sequence reads formed from the sequence reads such that each sequence read in a respective set of sequence reads corresponds to a subset of the nucleic acid represented by the bin corresponding to the respective set. Binomial tests identify bin pairs having more sequence reads with the same barcode in common than expected by chance. Probabilistic models determine structural variation likelihood from the sequence reads of these bin pairs.

Disclosed is a method of synchronizing media review on first and second nodes. The method may include the step of loading a media file having sequenced data segments into the first and second nodes. The media review may be related to processing the data segments for output. The method may also include the step of establishing a synchronized communication session between the first node and the second node. Thereafter, the method may include the step of executing a local media review command, and transmitting a remote media review command derived therefrom. The local and remote media review commands may be operative to regulate the media review of the media file on the first and second nodes.

A system, method, and computer program for controlling at least one infusion pump wherein the system comprises a first channel for delivering a first fluid, a second channel for delivering a second fluid, a first input for receiving channel sequence data wherein the channel sequence data identifies the sequence for delivering the first fluid from the first channel and the second fluid from the second channel, a second input for receiving first delivery data for the first channel and the second delivery data for the second channel, and a processor for controlling delivery of the first fluid from the first channel and the second fluid from the second channel according to the channel sequence data, the first delivery data, and the second delivery data.

The present invention is a system and method for performing real-time infection control over a computer network. The method comprises obtaining a sample of a microorganism at a health care facility, sequencing a first region of a nucleic acid from the microorganism sample, comparing the first sequenced region with historical sequence data stored in a database, determining a measure of phylogenetic relatedness between the microorganism sample and historical samples stored in the database, and providing infection control information based on the phylogenetic relatedness determination to the health care facility, thereby allowing the health care facility to use the infection control information to control or prevent the spread of an infection.

The present invention is a system and method for performing real-time infection control over a computer network. The method comprises obtaining a sample of a microorganism at a health care facility, sequencing a first region of a nucleic acid from the microorganism sample, comparing the first sequenced region with historical sequence data stored in a database, determining a measure of phylogenetic relatedness between the microorganism sample and historical samples stored in the database, and providing infection control information based on the phylogenetic relatedness determination to the health care facility, thereby allowing the health care facility to use the infection control information to control or prevent the spread of an infection.

The present invention provides an index structure for managing weighted-sequences in large databases. A weighted-sequence is defined as a two-dimensional structure in which each element in the sequence is associated with a weight. A series of network events, for instance, is a weighted-sequence because each event is associated with a timestamp. Querying a large sequence database by events' occurrence patterns is a first step towards understanding the temporal causal relationships among the events. The index structure proposed herein enables the efficient retrieval from the database of all subsequences (contiguous and non-contiguous) that match a given query sequence both by events and by weights. The index structure also takes into consideration the nonuniform frequency distribution of events in the sequence data.

Disclosed herein are methods and systems for classifying cell labels, for example identifying a signal cell label. In some embodiments, the method comprises: obtaining sequencing data of barcoded targets created using targets in cells barcoded using barcodes, wherein a barcode comprises a cell label and a molecular label. After ranking the cell labels, a minimum of a second derivative plot of a cumulative sum plot can be determined. Using the methods, a cell label can be classified as a signal cell label or a noise cell label based on the number of molecular labels with distinct sequences associated with the cell label and a cell label threshold.

Objective sequence data (10) which is primary sequence information on an objective protein is entered in an interaction site predicting device by the user. A secondary structure prediction simulation is executed on the objective sequence data (10) entered for secondary structure prediction programs (20a to 20d) that predict a secondary structure of a protein from primary sequence information of the protein. Results of secondary structure prediction (30a to 30d) from the respective secondary structure prediction programs (20a to 20d) are compared (60). Based on the comparison result, frustration of a local portion in the primary sequence information of the objective protein is calculated (70). An interaction site of the objective protein is predicted from the calculated frustration of the local portion (80).

Media monitoring and measurement systems and methods are disclosed. Some embodiments of the present invention provide a media measurement system and method that utilizes audience data to enhance content identifications. Some embodiments analyze media player log data to enhance content identification. Other embodiments of the present invention analyze sample sequence data to enhance content identifications. Other embodiments analyze sequence data to enhance content identification and / or to establish channel identification. Yet other embodiments provide a system and method in which sample construction and selection parameters are adjusted based upon identification results. Yet other embodiments provide a method in which play-altering activity of an audience member is deduced from content offset values of identifications corresponding to captured samples. Yet other embodiments provide a monitoring and measurement system in which a media monitoring device is adapted to receive a wireless or non-wireless audio signal from a media player, the audio signal also being received wirelessly by headphones of a user of the monitoring device.

Method includes receiving sequencing data including a plurality of sample reads that have corresponding sequences of nucleotides and assigning the sample reads to designated loci. The method also includes analyzing the assigned reads for each designated locus to identify corresponding regions-of-interest (ROIs) within the assigned reads. Each of the ROIs has one or more series of repeat motifs. The method also includes sorting the assigned reads based on the sequences of the ROIs such that the ROIs with different sequences are assigned as different potential alleles. The method also includes analyzing, for designated loci having multiple potential alleles, the sequences of the potential alleles to determine whether a first allele of the potential alleles is suspected stutter product of a second allele of the potential alleles.

Updating a software product by a plurality of patches. Sequencing data of each patch of the plurality of patches is received from a user such as a patch author. Each patch of the plurality of patches has a defined membership in a portion of the software product and has a defined order in the portion relative to one or more other patches that are members of the portion. The sequencing data indicates a portion of the software product of which the patch is a member and a relative ordering between the patch and one or more other members of the portion. A logical order of application for the plurality of patches is determined based on the received sequencing data. The plurality of patches is applied to the software product according to the determined logical order of application.

An embodiment of an identifier element for identifying an origin of a template nucleic acid molecule is described that comprises a nucleic acid element comprising a sequence composition that enables detection of an introduced error in sequence data generated from the nucleic acid element and correction of the introduced error, where the nucleic acid element is constructed to couple with the end of a template nucleic acid molecule and identifies an origin of the template nucleic acid molecule.

A system and method is provided for utilizing output-timing data to control at least one output timing parameter of a point-of-load (“POL”) regulator. Specifically, a power supply controller (“controller”) is adapted to transmit output-timing data to at least one POL regulator. In one embodiment of the present invention, each POL regulator includes an output builder, a control unit and a storage device. The control unit is adapted to store the output-timing data in the storage device. The control unit and the output builder are then adapted to produce an output having at least one output timing parameter in accordance with the output-timing data. Examples of output-timing data include sequencing data, turn-on data, turn-off data, termination data, slew-rate data, etc. For example, a POL regulator may be adapted to utilize output-timing data, or a portion thereof (e.g., slew-rate data), to generate an output having a particular slew rate. Similarly, a POL regulator may be adapted to utilize output-timing data, or a portion thereof (e.g., sequencing data, turn-on data, etc.), to determine (or calculate) a period of time to wait (e.g., delay period) before the output is generated. In other words, output-timing data can be used to produce a series of outputs in a particular order, or sequence.