62 results about "Short read" patented technology

The disclosure provides methods of generating paired reads in sequencing-by-synthesis process, particularly, in systems with relatively short read lengths (e.g., 15-35 bases), such as for example, in single molecule sequencing by synthesis. Several implementations of the methods are provided. Of particular advantage are the methods that permit re-sequencing of the template, which yields lower error rates. The invention further provides methods of using paired reads, for example, for positioning them over repeats or for assembly into large sequences, including whole genome assembly.

Certain embodiments of the invention provide systems and methods for the automated assembly of DNA sequence data into contiguous DNA segments using a computer a system. DNA sequence data is entered into the system. The system indexes and groups a plurality of DNA fragment reads utilizing an anchor sequence and consolidates the fragments into larger sequences by merging the fragment reads within a group.

A scalable FPGA-based solution to the short read mapping problem in DNA sequencing is disclosed which greatly accelerates the task of aligning short length reads to a known reference genome. A representative system comprises one or more memory circuits storing a plurality of short reads and a reference genome sequence; and one or more field programmable gate arrays configured to select a short read; to extract a plurality of seeds from the short read, each seed comprising a genetic subsequence of the short read; for each seed, to determine at least one candidate alignment location (CAL) in the reference genome sequence to form a plurality of CALs; for each CAL, to determine a likelihood of the short read matching the reference genome sequence in the vicinity of the CAL; and to select one or more CALs having the currently greater likelihood of the short read matching the reference genome sequence.

Various short reads can be grouped and identified as coming from a same long DNA fragment (e.g., by using wells with a relatively low-concentration of DNA). A histogram of the genomic coverage of a group of short reads can provide the edges of the corresponding long fragment (pulse). The knowledge of these pulses can provide an ability to determine the haploid genome and to identify structural variations.

In multilayer optical discs and high-speed optical discs, the amount of reproduction light per unit time greatly decreases and the reproduction signal quality (S/N) significantly drops due to the low effective reflectivity and the short read time of the medium. These problems are solved by causing reflected signal light from the optical disc and reference light, which is separated from the same light source and introduced into a detector without being shone onto the optical disc, to interference with each other on the detector. Detector outputs having four different interference states are simultaneously obtained, the interference states being displaced at intervals of 90° in terms of the phase relationship between the reference light and the signal. Based on a operation of the four detector outputs, a reproduction signal can be obtained that is stable at all times and amplified with high quality, even when there is an optical path length variation due to disc undulations.

The invention discloses a transcriptome-based tumor antigen identification method. The method comprises four steps of: obtaining an RNA sample of a patient tumor tissue, and carrying out library construction and amplification on the RNA sample to obtain an RNA sample sequencing result of the tumor tissue; aligning short read segments of the RNA sample sequencing result to a human reference genometo obtain an RNA alignment result; calculating gene expression quantity according to the RNA alignment result, and carrying out mutation detection and prediction of fusion gene events according to theRNA alignment result; and predicting transcriptome HLA typing according to the alignment result, wherein calculation of the gene expression quantity, mutation detection and prediction of the fusion gene events are carried out according to a specified order or simultaneously carried out; and using the gene expression quantity of a transcriptome sample, depth of transcriptome mutation sites in a whole-exon sequencing sample and binding force of neonatal short peptides and the patient HLA typing as an analysis result to submit the same to a downstream analyst. The invention provides the method capable of identifying a tumor-specific antigen of an individual sample from tumor patient transcriptome NGS data.

The present invention provides improved methods, compositions and kits for short read next generation sequencing (NGS). The methods, compositions and kits of the present invention enable phasing of two or more nucleic acid sequences in a sample, i.e. determining whether the nucleic acid sequences (typically comprising regions of sequence variation) are located on the same chromosome and/or the same chromosomal fragment. Phasing information is obtained by performing multiple, successive sequencing reactions from the same immobilized nucleic acid template. The methods, compositions and kits provided herein are useful, for example, for haplotyping, SNP phasing, or for determining downstream exons in RNA-seq.

A Flash-EPROM type memory cell with a short read time and a "very low supply voltage." The memory cell has the additional advantage of using less power, therefore generating less heat and allowing a denser integrated circuit. The memory cell comprises a floating-gate transistor whose source is coupled to the drain of a selection transistor. The floating-gate transistor is in a depleted state when the memory cell is "erased." The read voltage applied to the control gate of the floating-gate transistor is substantially equal to a general supply voltage which is in the range of 1.5 volts. The gate of the selection transistor receives a bias voltage at least equal to its conduction threshold. The gate of the selection transistor can also receive a bias voltage higher than the read voltage, which will speed up the read time further. A Flash-EPROM incorporating this memory cell is also provided.

As memory geometries continue to scale down, current density of magnetic tunnel junctions (MTJs) make conventional low current reading scheme problematic with regard to performance and reliability. A body-voltage sense circuit (BVSC) short pulse reading (SPR) circuit is described using body connected load transistors and a novel sensing circuit with second stage amplifier which allows for very short read pulses providing much higher read margins, less sensing time, and shorter sensing current pulses. Simulation results (using 65-nm CMOS model SPICE simulations) show that our technique can achieve 550 mV of read margin at 1 ns performance under a 1V supply voltage, which is greater than reference designs achieve at 5 ns performance.

The present teachings relate to improved methods, kits, and compositions for making nucleic acid libraries and sequencing nucleic acids. In some embodiments, directionally defined concatamers are generated, facilitating sequencing efforts.

Provided are a digital photographing apparatus in which a read-out mode may be changed when capturing a moving image, and a method of controlling the digital photographing apparatus. The method includes capturing a moving image having a predetermined frame rate in a first read-out mode, estimating a brightness of surroundings and then determining a shutter speed of a frame to be currently captured based on the estimated brightness of the surroundings, determining whether or not an exposure time that is dependent on the shutter speed is longer than a predetermined time period, and changing the first read-out mode to a second read-out mode that has a shorter read-out time than the first read-out mode when the exposure time is longer than the predetermined time period.

A technique for executing alignment algorithms on a SIMT processing environment is disclosed. An alignment algorithm having multiple stages is executed within the SIMT environment such that a different thread group executes each stage of the algorithm. Each thread group performs a different set of alignment operations related to a different stage of alignment algorithm for a group of short reads. In such a manner, the thread groups operate in unison to perform all the operations related to each stage of the alignment algorithm on every short read in the group of short reads.

The invention relates to the radio frequency automatic identification technology of the field of the backscattering communication system, discloses an RFID read-write system capable of enhancing RFID read-write distance and a read-write method thereof, and solves the problems in the prior art that a passive RFID system is short in read-write distance. The RFID read-write method comprises the following steps that a. a reader-writer transmits a pilot signal to a tag; b. the tag backscatters the pilot signal; c. the reader-writer receives the pilot signal backscattered by the tag; d. the reader-writer estimates a backscattering channel; e. the reader-writer transmits an energy beam forming signal to the tag; f. the tag collects radio frequency signal energy; g. the reader-writer transmits an unmodulated carrier signal; h. and the tag transmits information back to the reader-writer through backscattering modulation by utilizing the collected energy. The read-write range of the RFID reader-writer can be greatly enhanced without increasing energy consumption of the transmitting end or increasing complexity of the tag so that the severe defect of restriction of short read-write distance of the RFID system can be effectively solved, and thus the RFID read-write system and the read-write method are suitable for realization of long-distance RFID read-write.

Techniques perform de novo assembly. The assembly can use labels that indicate origins of the nucleic acid molecules. For example, a representative set of labels identified from initial reads that overlap with a seed can be used. Mate pair information can be used. A sequence read that aligns to an end of a contig can lead to using the other sequence read of a mate pair, and the other sequence read can be used to determine which branch to use to extend, e.g., in an external cloud or helper contig. A kmer index can include labels indicating an origin of each of the nucleic acid molecules that include each kmer, memory addresses of the reads that correspond to each kmer in the index, and a position in each of the mate pairs that includes the kmer. Haploid seeds can also be determined using polymorphic loci identified in a population.

The invention relates to a method for developing SSRs (simple sequence repeats) molecular markers of genome of an ammopiptanthus mongolicus (Maxim.) Chengf. plant, wherein the method comprises the following steps: (1) establishing a primary sequencing library for genome DNA of a species sample sampled from a first production area, and conducting high-throughput sequencing so as to obtain Short Reads sequencing data; (2) filtering Reads obtained from sequencing and conducting sequence assembling so as to obtain Contigs; (3) conducting SSRs identification on Contigs sequences; and (4) verifying the SSRs in a Unigene sequence of a same species derived from a second production area, and conducting screening so as to obtain the SSRs having polymorphism. The high-throughput SSRs molecular marker discovering method provided by the invention is applicable to such researches as genetic map construction, QTL (quantitative trait loci) location, genetic diversity analysis and the like of the plant species.

The invention relates to a Zr:Fe:LiNbO3 crystal and the preparing method thereof, relating to a crystal and the preparing method thereof. And the crystal is made of ZrO2, Fe2O3, LiCO3 and Nb2O5 with the same purity of 99.99%, where the ZrO2 doping quantity is 2-6mol%, the Fe2O3 doping concentration is 0.01-0.04wt%, and the molar ratio of Li to Nb is 0.946. and the preparing method comprises the steps of: 1. weighing ZrO2, Fe2O3, LiCO3 and Nb2O5 and fully mixing them; 2. placing the ready-mixed raw materials into a Pt pot, and making crystal growth by Czochralski method; 3. polarizing the obtained crystals in the step 2; then accurately orienting the polarized crystals and cutting by Y surface and making optical quality polishing on the crystal surfaces and obtaining Zr:Fe:LiNbO3 crystals. And the Zr:Fe:LiNbO3 crystal can act as huge-capacity holographic memory. And the invention has advantages of small reduced amplitude of diffraction efficiency, short read-in time, high flexibility and strong optical loss resistance.