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41. 发明申请

US20150120256A1 METHOD OF RECONSTRUCTING HAPLOTYPE OF DIPLOID AND SYSTEM THEREOF 审中-公开
标题翻译：重复二倍体皮脂的方法及其系统
公开(公告)号：US20150120256A1
公开(公告)日：2015-04-30
申请号：US14369604
申请日：2012-05-31
申请人： Shujia Huang , Peng Sun , Honglong Wu , Jian Wang , Jun Wang , Huanming Yang
发明人： Shujia Huang , Peng Sun , Honglong Wu , Jian Wang , Jun Wang , Huanming Yang
IPC分类号： G06F19/12 , G06F17/16 , G06F17/50
CPC分类号： G16B5/00 , G06F17/16 , G06F17/5009 , G16B20/00 , G16B40/00
摘要： Provided is a method and system of reconstructing a haplotype of a diploid. The method can include constructing a matrix of sequence fragments consisting of ternary character based on sequence fragments comprising at least one common site, wherein in the matrix of sequence fragments, two allelic bases of an SNP site in chromosome fragments are labeled with A and B respectively; initializing two fragment sets of based on the matrix of sequence fragments; determining an objective function and an initial reference temperature; performing a process of simulated annealing based on the objective function and the initial reference temperature, and outputting final sets until a convergence criteria is achieved; inferring a haplotype based on the final sets by means of minimum error correction.
摘要翻译：提供了重建二倍体的单体型的方法和系统。该方法可以包括构建基于包含至少一个共同位点的序列片段的由三元字符组成的序列片段的矩阵，其中在序列片段的基序中，染色体片段中的SNP位点的两个等位基因分别用A和B标记 ; 基于序列片段的矩阵初始化两个片段集合; 确定目标函数和初始参考温度; 基于目标函数和初始参考温度执行模拟退火过程，并输出最终集合直到达到收敛标准; 通过最小误差校正推导出基于最终集合的单倍型。

42. 发明申请

US20150120204A1 TRANSCRIPTOME ASSEMBLY METHOD AND SYSTEM 审中-公开
标题翻译：代码汇编方法和系统
公开(公告)号：US20150120204A1
公开(公告)日：2015-04-30
申请号：US14394135
申请日：2012-04-13
申请人： Gengxiong Wu , Weihua Huang , Yinlong Xie , Jingbo Tang , Jun Wang , Jian Wang , Huanming Yang
发明人： Gengxiong Wu , Weihua Huang , Yinlong Xie , Jingbo Tang , Jun Wang , Jian Wang , Huanming Yang
IPC分类号： G06F19/22 , G06F19/20
CPC分类号： G16B30/00 , G16B25/00
摘要： Provided is a transcriptome assembly method, comprising the following steps of: constructing a sequencing sample transcriptome read into a de Brujin graph; performing filtering and linearization processing on the de Brujin graph, so as to form continuous contigs; obtaining association among the contigs, and filtering association data; performing linearization processing on a continuous sequence without bifurcation; outputting a contig sequence; comparing the read and an end pairing read with the output contig sequence, so as to obtain information between the read and the contig; establishing connections among the contigs, so as to construct a graph with the contigs as points and the connections as edges; pre-processing and dividing the obtained graph, so as to obtain independent sub-graphs; and outputting a transcript according to the sub-graphs. Further provided is a transcriptome assembly system based on the method.
摘要翻译：提供了一种转录组装方法，包括以下步骤：构建读取到de Brujin图中的测序样本转录组; 对de Brujin图进行滤波和线性化处理，形成连续重叠群; 获得重叠群之间的关联，并过滤关联数据; 对没有分岔的连续序列进行线性化处理; 输出重叠序列; 将读取和结束配对读取与输出contig序列进行比较，以便获得读取和重叠数据之间的信息; 在重叠群之间建立连接，以便以重叠群构建点作为边缘的连接; 预处理和划分获得的图，以获得独立的子图; 并根据子图输出抄本。还提供了一种基于该方法的转录组装系统。

43. 发明申请

US20140256563A1 HIGH THROUGHPUT METHYLATION DETECTION METHOD 有权
标题翻译：高通量甲基化检测方法
公开(公告)号：US20140256563A1
公开(公告)日：2014-09-11
申请号：US14119266
申请日：2012-05-22
申请人： Huijuan Luo , Guanyu Ji , Hui Jiang , Mingzhi Wu , Jihua Sun , Renhua Wu , Junwen Wang , Fei Gao
发明人： Huijuan Luo , Guanyu Ji , Hui Jiang , Mingzhi Wu , Jihua Sun , Renhua Wu , Junwen Wang , Fei Gao
IPC分类号： C12Q1/68 , C12N15/10
CPC分类号： C12Q1/6874 , C12N15/1065 , C12Q1/6806 , C12Q1/6869 , C40B50/06 , C12Q2523/125 , C12Q2525/191 , C12Q2535/122 , C12Q2537/159
摘要： Provided is a high throughput methylation detection method, particularly a combined sequence capture and bisulfite sequencing method. The method accurately and effectively analyzes the methylation status of the target area in several samples simultaneously, lowers the difficulty of probe design, enhances operation and application feasibility, and enables high throughput methylation detection of high accuracy on interested target sequences and areas in a complete genome. The method is targeted and conserves energy and time.
摘要翻译：提供了高通量甲基化检测方法，特别是组合的序列捕获和亚硫酸氢盐测序方法。该方法同时精确有效地分析了几个样本中目标区域的甲基化状态，降低了探针设计的难度，提高了操作和应用的可行性，并且使得在完整基因组中有兴趣的靶序列和区域具有高准确度的高通量甲基化检测。该方法是针对性的，节约能源和时间。

44. 发明申请

US20140194300A1 Method and device for genetic map construction, method and device for haplotype analysis 有权
标题翻译：用于遗传图谱构建的方法和装置，用于单倍型分析的方法和装置
公开(公告)号：US20140194300A1
公开(公告)日：2014-07-10
申请号：US14240955
申请日：2012-08-24
申请人： Luting Song , Di Shao , Zequn Zheng , Zhijun Zheng , Kui Wu , Shuheng Liang , Ye Tao , Yong Hou
发明人： Luting Song , Di Shao , Zequn Zheng , Zhijun Zheng , Kui Wu , Shuheng Liang , Ye Tao , Yong Hou
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q1/6874 , C12Q1/6881 , C12Q2600/172 , G06F19/20 , G06F19/22
摘要： Provided are the method and device for genetic map construction and the method and device for haplotype determination of a single cell. Wherein the method for genetic map construction includes: whole genome sequencing for at least a single cell from a same species, aligning the sequencing data to reference sequences respectively to determine genotypes of SNP sites, determining male parent a/female parent b typing results of SNP genotypes of a single cell based on the genotypes of SNP sites, dividing the chromosome of the species into linkage regions based on the male parent a/female parent b typing results of SNP genotypes, determining the variation ratio of a/b between two linkage regions to obtain recombination rate between every two continuous linkage regions, determining recombination map of a single cell according to the recombination rate, wherein the boundary site of a and b is the recombination site, determining the recombination rate of each recombination rate based on the recombination map to construct a genetic map of the species.
摘要翻译：提供遗传图谱构建的方法和装置以及单细胞单体型确定的方法和装置。遗传图谱构建方法包括：对同一物种的至少一个细胞进行全基因组测序，分别将测序数据与参照序列进行比对，以确定SNP位点的基因型，确定SNP的雄性亲本a /雌性亲本B分型结果基于SNP位点基因型的单细胞基因型，根据SNP基因型的雄性亲本a /雌性亲本B分型结果将该物种的染色体分为连锁区，确定两个连锁区之间a / b的变异比以获得每两个连续连锁区域之间的重组率，根据复合率确定单个细胞的重组图谱，其中a和b的边界位点是重组位点，基于重组图确定每个重组速率的重组率构建该物种的遗传图谱。

45. 发明申请

US20140188397A1 Methods of acquiring genome size and error 审中-公开
标题翻译：获取基因组大小和误差的方法
公开(公告)号：US20140188397A1
公开(公告)日：2014-07-03
申请号：US14118109
申请日：2011-05-17
申请人： BGI Tech Solutions Co., Ltd.
发明人： Wei Fan , Binghang Liu , Zhenyu Li , Jun Wang
IPC分类号： G06F19/10
CPC分类号： G16B99/00 , G16B30/00
摘要： Provided is a method of acquiring genome size. The method comprises steps of sequencing random fragments of whole genome, acquiring all of k-mer information including k-mer depth, counting frequency of each k-mer depth value so as to determine expected k-mer depth, and acquiring the genome size by dividing the sum of k-mers by the expected k-mer depth. The method is convenient, rapid, and cost-effective. Also provided is a method of acquiring error of sequencing genome based on all of k-mer information including k-mer depth.
摘要翻译：提供了获取基因组大小的方法。该方法包括对全基因组随机片段进行测序的步骤，获取所有k-mer信息，包括k-mer深度，每个k-mer深度值的计数频率，以便确定预期的k-mer深度，以及通过将k-mers的总和除以预期的k-mer深度。该方法方便快捷，性价比高。还提供了基于包括k-mer深度的所有k-mer信息来获取测序基因组的错误的方法。

46. 发明公开

EP2377949A4 CONSTRUCTION METHOD AND SYSTEM OF FRAGMENTS ASSEMBLING SCAFFOLD, AND GENOME SEQUENCING DEVICE 有权转让
标题翻译：基因测序施工方法和系统FRAGMENTASSEMBLIERUNGSGERÜST和设备
公开(公告)号：EP2377949A4
公开(公告)日：2014-12-17
申请号：EP09831393
申请日：2009-12-11
申请人： BGI TECH SOLUTIONS CO LTD
发明人： NI PEIXIANG , FANG XIAODONG , WANG JUN , YANG HUANMING , WANG JIAN
IPC分类号： G06F19/22 , C12Q1/68
CPC分类号： G06F19/22
摘要： The present invention relates to gene engineering filed, and provides a genome sequencing device, construction method of fragments assembling scaffold and system thereof. The method comprises the following steps: mapping the double-barreled data obtained through sequencing to contigs; calculating the mean length between contigs based on multiple pairs of double-barreled data mapped to contigs, which is taken as the gap size between contigs; constructing scaffold based on gap size between contig and the double-barreled relation between contigs; and obtaining complete scaffold graph. Since the mean length between contigs is calculated from multiple pairs of double-barreled data and is taken as the gap size between contigs, the estimation precision of gap size between contigs is improved greatly. It can be used for genome sequencing including short sequencing read length to finish task of assembling sequencing fragments.

47. 发明公开

EP2631336A1 DNA LIBRARY AND PREPARATION METHOD THEREOF, AND METHOD AND DEVICE FOR DETECTING SNPS 有权转让
标题翻译： DNA文库及其制造方法和SNP的检测方法及装置
公开(公告)号：EP2631336A1
公开(公告)日：2013-08-28
申请号：EP11843141.0
申请日：2011-09-21
申请人： BGI Shenzhen Co., Limited , BGI Shenzhen
发明人： DU, Ye , ZHAO, Meiru , CHEN, Ying , WU, Jinghua , TIAN, Geng , WANG, Jun
IPC分类号： C40B50/06 , C40B40/08 , C40B20/04 , C12N15/11 , C12Q1/68
CPC分类号： C12Q1/683 , C12N15/1093 , C12Q1/6869 , C12Q1/6883 , C12Q2521/313 , C12Q2525/191 , C40B50/06
摘要： A DNA library, and a preparing method thereof, a method of determining DNA sequence information, an apparatus and a kit for detecting SNPs, and a method for genotyping may be provided. The method for preparing the DNA library may comprise the steps of: digesting a genomic DNA sample using a restriction endonuclease to obtain a digested product, wherein the restriction endonuclease comprises at least one selected from the group consisting of Mbo II and Tsp 451; separating the digested product to obtain DNA fragments having a length of 100 bp to 1,000 bp; end-repairing the DNA fragments to obtain an end-repaired DNA fragments; adding a base A to the end of the end-repaired DNA fragments to obtain DNA fragments having a terminal base A; and ligating the DNA fragments having the terminal base A with sequencing adaptors to obtain the DNA library.
摘要翻译：可以提供DNA文库，以及它们的制备方法，确定性采矿DNA序列信息的方法，以装置和用于检测单核苷酸多态性的试剂盒，以及用于基因分型的方法。用于制备DNA文库可以包括以下步骤的方法：用限制性内切酶，以获得消化产物消化基因组DNA样品，worin限制性内切酶包括至少一种选自II姆博和Tsp的451的选择; 分离消化产物，以获得具有100 bp的长度至1000碱基对的DNA片段; 最终修复的DNA片段，以获得在末端修复的DNA片段; 加入碱A到末端修复的DNA片段的末端，以获得具有端子基部的DNA片段; 并连接具有测序衔接端子座甲以获得DNA文库中的DNA片段。

48. 发明公开

EP2725125A4 HIGH THROUGHPUT METHYLATION DETECTION METHOD 有权
标题翻译：具有高吞吐量甲基化检测方法
公开(公告)号：EP2725125A4
公开(公告)日：2014-12-24
申请号：EP12789707
申请日：2012-05-22
申请人： BGI TECH SOLUTIONS CO LTD
发明人： LUO HUIJUAN , JI GUANYU , JIANG HUI , WU MINGZHI , SUN JIHUA , WU RENHUA , WANG JUNWEN , GAO FEI
IPC分类号： C40B50/06 , C12N15/11 , C12Q1/68 , C40B20/04 , C40B40/08
CPC分类号： C12Q1/6874 , C12N15/1065 , C12Q1/6806 , C12Q1/6869 , C40B50/06 , C12Q2523/125 , C12Q2525/191 , C12Q2535/122 , C12Q2537/159
摘要： Provided is a high throughput methylation detection method, particularly a combined sequence capture and bisulfite sequencing method. The method accurately and effectively analyzes the methylation status of the target area in several samples simultaneously, lowers the difficulty of probe design, enhances operation and application feasibility, and enables high throughput methylation detection of high accuracy on interested target sequences and areas in a complete genome. The method is targeted and conserves energy and time.

49. 发明授权

EP2377949B1 CONSTRUCTION METHOD AND SYSTEM OF FRAGMENTS ASSEMBLING SCAFFOLD 有权转让
公开(公告)号：EP2377949B1
公开(公告)日：2018-11-21
申请号：EP09831393.5
申请日：2009-12-11
申请人： BGI Tech Solutions Co., Ltd.
发明人： NI, Peixiang , FANG, Xiaodong , WANG, Jun , YANG, Huanming , WANG, Jian
IPC分类号： G06F19/22 , C12Q1/68
CPC分类号： G06F19/22
摘要： The present invention relates to gene engineering filed, and provides a genome sequencing device, construction method of fragments assembling scaffold and system thereof. The method comprises the following steps: mapping the double-barreled data obtained through sequencing to contigs; calculating the mean length between contigs based on multiple pairs of double-barreled data mapped to contigs, which is taken as the gap size between contigs; constructing scaffold based on gap size between contig and the double-barreled relation between contigs; and obtaining complete scaffold graph. Since the mean length between contigs is calculated from multiple pairs of double-barreled data and is taken as the gap size between contigs, the estimation precision of gap size between contigs is improved greatly. It can be used for genome sequencing including short sequencing read length to finish task of assembling sequencing fragments.

50. 发明授权

EP2377948B1 ERROR CORRECTING METHOD OF TEST SEQUENCE, CORRESPONDING SYSTEM AND GENE ASSEMBLY EQUIPMENT 有权转让
标题翻译：测试序列中，相应的系统及设备的基因合成纠错方法
公开(公告)号：EP2377948B1
公开(公告)日：2016-05-18
申请号：EP09831391.9
申请日：2009-12-11
申请人： BGI Tech Solutions Co., Ltd.
发明人： WANG, Jun , YANG, Huanming , WANG, Jian
IPC分类号： G06F19/22 , G06F19/24
CPC分类号： G06F19/24 , C12Q1/6874 , G06F19/22

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