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1. 发明授权

US10395757B2 Parental genome assembly method 有权
公开(公告)号：US10395757B2
公开(公告)日：2019-08-27
申请号：US14361865
申请日：2011-12-02
申请人： Weiming He , Shancen Zhao , Xuemei Zhang , Yingrui Li , Jun Wang , Jian Wang , Huanming Yang
发明人： Weiming He , Shancen Zhao , Xuemei Zhang , Yingrui Li , Jun Wang , Jian Wang , Huanming Yang
IPC分类号： G16B20/00 , C12Q1/6869 , C12Q1/6895 , G16C99/00
摘要： Provided is a parental genome assembly method, comprising: using the sequencing data of parental selfing line progeny population to assemble and perfect the parental genome data. Also provided is a device for implementing the method.

2. 发明申请

US20150205913A1 PARENTAL GENOME ASSEMBLY METHOD 审中-公开
标题翻译：亲本基因组装方法
公开(公告)号：US20150205913A1
公开(公告)日：2015-07-23
申请号：US14361865
申请日：2011-12-02
申请人： Weiming He , Shancen Zhao , Xuemei Zhang , Yingrui Li , Jun Wang , Jian Wang , Huanming Yang
发明人： Weiming He , Shancen Zhao , Xuemei Zhang , Yingrui Li , Jun Wang , Jian Wang , Huanming Yang
IPC分类号： G06F19/18 , C12Q1/68
CPC分类号： G16B20/00 , C12Q1/6869 , C12Q1/6895 , C12Q2535/122 , G16C99/00
摘要： Provided is a parental genome assembly method, comprising: using the sequencing data of parental selfing line progeny population to assemble and perfect the parental genome data. Also provided is a device for implementing the method.
摘要翻译：提供了一种亲本基因组装配方法，其包括：使用亲本自交系后代群体的测序数据来组合和完善亲本基因组数据。还提供了一种用于实现该方法的装置。

3. 发明申请

US20140350866A1 Method of Gap Closing in Nucleotide Sequence and Apparatus Thereof 审中-公开
公开(公告)号：US20140350866A1
公开(公告)日：2014-11-27
申请号：US14361158
申请日：2011-11-29
申请人： Binghang Liu , Zhenyu Li , Yanxiang Chen , Yingrui Li , Jian Wang , Jun Wang , Huanming Yang
发明人： Binghang Liu , Zhenyu Li , Yanxiang Chen , Yingrui Li , Jian Wang , Jun Wang , Huanming Yang
IPC分类号： G06F19/16
CPC分类号： G16B15/00 , C12Q1/6869 , G16B30/00 , C12Q2537/165
摘要： Provided is a method of gap closing in nucleotide sequence. The nucleic acid sequence comprises a first contig at one end of a gap in an unassembled region, and a second contig at the other end of the gap in the unassembled region. The method comprises: selecting reads having an overlap with one end of the first contig close to the gap as a set of reads for gap closing; selecting reads having a shortest overlap with the first contig in the set of reads for gap closing as a candidate read; determining whether reads having an overlapping length with the first contig shorter than an overlapping length between the candidate read and the first contig present in the set of reads for gap closing, and determining whether reads having no overlapping relationship with the candidate read present in the set of reads for gap closing; obtaining a result of presenting an extension conflict, and determining an unconfident candidate read, if reads having an overlapping length with the first contig shorter than an overlapping length between the candidate read and the first contig present in the set of reads for gap closing, reads having no overlapping relationship with the candidate read present in the set of reads for gap closing, or both reads having an overlapping length with the first contig shorter than an overlapping length between the candidate read and the first contig, and reads having no overlapping relationship with the candidate read present in the set of reads for gap closing; reselecting the candidate read until obtaining a confident candidate read, if the candidate read is unconfident; connecting the confident candidate read to the first contig, to form a new first contig; determining whether one end of the new first contig close to the gap has an overlap with one end of the second contig close to the gap; performing the step of selecting the set of reads for gap closing on the basis of the new first contig, if the one end of the new first contig close to the gap has no overlap with the one end of the second contig close to the gap, wherein the first contig in the step of selecting the set of reads for gap closing is replaced with the new first contig; connecting the new first contig to the second contig to complete gap closing, if one end of the new first contig close to the gap has an overlap with one end of the second contig close to the gap.

4. 发明申请

US20150120210A1 METHOD AND DEVICE FOR LABELLING SINGLE NUCLEOTIDE POLYMORPHISM SITES IN GENOME 审中-公开
标题翻译：在基因组中标记单个核苷酸多态性位点的方法和装置
公开(公告)号：US20150120210A1
公开(公告)日：2015-04-30
申请号：US14369318
申请日：2011-12-29
申请人： Ye Tao , Zequn Zheng , Zihao Feng , Yingrui Li , Huanming Yang , Jun Wang , Jian Wang
发明人： Ye Tao , Zequn Zheng , Zihao Feng , Yingrui Li , Huanming Yang , Jun Wang , Jian Wang
IPC分类号： G06F19/22
CPC分类号： G16B30/00 , C12Q1/6869 , G16B20/00 , C12Q2535/131
摘要： Disclosed are a method and a device for labelling single nucleotide polymorphism site in a genome. The above-mentioned method comprises: the single-end RAD sequences from the genomes of two individuals are obtained; the single-end RAD sequences are filtered to remove unqualified sequences; the sequencing depth of the sequences from the genomes of two individuals is aligned in pairs and without gaps to determine the SNP sites.
摘要翻译：公开了用于在基因组中标记单核苷酸多态性位点的方法和装置。上述方法包括：获得来自两个个体的基因组的单末端RAD序列; 过滤单端RAD序列以除去不合格序列; 来自两个个体的基因组的序列的测序深度成对排列并且没有间隙以确定SNP位点。

5. 发明授权

US09857377B2 Method for quantification of proteome 有权
公开(公告)号：US09857377B2
公开(公告)日：2018-01-02
申请号：US14369825
申请日：2011-12-31
申请人： Haiyi Zhao , Dahai Jiang , Bo Wen , Jian Wang , Jun Wang , Huanming Yang , Jin Zi , Yan Ren , Siqi Liu
发明人： Haiyi Zhao , Dahai Jiang , Bo Wen , Jian Wang , Jun Wang , Huanming Yang , Jin Zi , Yan Ren , Siqi Liu
IPC分类号： G01N33/68 , G06F19/18 , H01J49/00
CPC分类号： G01N33/6848 , G01N33/68 , G01N2570/00 , G06F19/18 , H01J49/0036
摘要： The present invention relates to a method for quantifying the relative content of a protein in a sample. The present invention also relates to a method for comprising the relative content of a protein in at least two samples.

6. 发明申请

US20140249038A1 Method of detecting a pre-determined event in a nucleic acid sample and system thereof 审中-公开
标题翻译：检测核酸样品中的预定事件的方法及其系统
公开(公告)号：US20140249038A1
公开(公告)日：2014-09-04
申请号：US14351468
申请日：2011-12-21
申请人： Hui Jiang , Fang Chen , Huijuan Ge , Peipei Li , Xuchao Li , Jian Wang , Jun Wang , Huanming Yang , Xiuqing Zhang
发明人： Hui Jiang , Fang Chen , Huijuan Ge , Peipei Li , Xuchao Li , Jian Wang , Jun Wang , Huanming Yang , Xiuqing Zhang
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6869 , C12Q1/6883 , C12Q2600/156
摘要： Disclosed are a method of detecting a pre-determined event in a nucleic acid sample and a system thereof. The method of detecting the pre-determined event in the nucleic acid sample comprises the following steps: constructing a sequencing-library for the nucleic acid sample; sequencing the sequencing-library to obtain a sequencing result consisting of a plurality of sequencing data; determining the sequencing data from a pre-determined region; and determining an occurrence of the pre-determined event in the nucleic acid sample based on a composition of the sequencing data from the pre-determined region.
摘要翻译：公开了一种在核酸样品及其系统中检测预定事件的方法。检测核酸样品中预先确定事件的方法包括以下步骤：构建核酸样品的测序文库; 测序序列库以获得由多个测序数据组成的测序结果; 确定来自预定区域的测序数据; 以及基于来自预定区域的测序数据的组成确定核酸样品中预定事件的发生。

7. 发明授权

US08751165B2 Error correcting method of test sequence, corresponding system and gene assembly equipment 有权
标题翻译：测试序列错误纠正方法，相应的系统和基因组装设备
公开(公告)号：US08751165B2
公开(公告)日：2014-06-10
申请号：US13132038
申请日：2009-12-11
申请人： Jun Wang , Huanming Yang , Jian Wang
发明人： Jun Wang , Huanming Yang , Jian Wang
IPC分类号： G01N33/48 , G06F19/00 , G06F19/24
CPC分类号： G06F19/24 , C12Q1/6874 , G06F19/22
摘要： The present invention provides an error correcting method of test sequence, which involves receiving test sequences, configuring high frequency short string list based on a preset high frequency threshold value, traversing each received test sequence, searching an area with the largest number of continuous high frequency short strings on each test sequence in combination with high frequency short string list, configuring whole left sequence and/or right sequence of high frequency short strings at left side and/or right side of searched area according to corresponding received test sequence and high frequency short string list, and constituting corresponding test sequence according to configured left and/or right sequence and searched area. The present invention also provides corresponding error correcting system of test sequence and gene assembly equipment.
摘要翻译：本发明提供一种测试序列的纠错方法，其包括接收测试序列，基于预设的高频阈值配置高频短串列表，遍历每个接收的测试序列，搜索具有最大数目的连续高频区域每个测试序列上的短串组合高频短串列表，根据相应的接收测试序列和高频短信配置搜索区域的左侧和/或右侧的全部左序列和/或右序列的高频短串字符串列表，并根据配置的左和/或右序列和搜索区域构成对应的测试序列。本发明还提供了相应的测试序列和基因组装设备的纠错系统。

8. 发明申请

US20140323320A1 METHOD OF DETECTING FUSED TRANSCRIPTS AND SYSTEM THEREOF 审中-公开
公开(公告)号：US20140323320A1
公开(公告)日：2014-10-30
申请号：US14369566
申请日：2011-12-31
申请人： Wenlong Jia , Kunlong Qiu , Guangwu Guo , Minghui He , Jun Wang , Jian Wang , Huanming Yang
发明人： Wenlong Jia , Kunlong Qiu , Guangwu Guo , Minghui He , Jun Wang , Jian Wang , Huanming Yang
IPC分类号： G06F19/22
CPC分类号： G16B30/00 , C12Q1/6869 , C12Q2535/122
摘要： Provided is a method of detecting method of detecting fusion transcripts in a sample to be analyzed. The method may comprises: subjecting the sample to be analyzed containing a RNA transcriptome to paired-end sequencing, to obtain paired-end RNA-Seq data of the sample to be analyzed; aligning the paired-end RNA-Seq data to a human reference genome sequence, to obtain first paired-end mapped reads, first single-end mapped reads, and first unmapped reads; evaluating an insertsize between two ends of the paired-end mapped reads by means of the first paired-end mapped reads, to obtain a proportion of paired-end mapped reads with overlapped 3′-ends; aligning the first unmapped reads to annotated transcripts, to obtain second single-end mapped reads and second unmapped reads; aligning the second unmapped reads to the annotated transcripts, to filter out unmapped reads caused by indel and obtain third unmapped reads; merging all single-end mapped reads, to obtain a set of single-end mapped reads; obtaining a gene pair linked by a cross-read as a primary set of candidate gene pairs based on the set of single-end mapped reads and combining with a relationship of the mapped paired-end reads; subjecting the primary set of candidate gene pairs to a filtration, to obtain a candidate set of fused gene pairs; bisecting the third unmapped read, to obtain a half-unmapped read; aligning the half-unmapped read to a gene-junction sequence in the candidate set of fused gene pairs, to obtain a potent region of a fused junction site in the gene in which the half-unmap read locates; outputting original reads of mapped half-unmapped reads, to obtain useful unmapped reads; subjecting the candidate set of fused gene pairs to a fusion simulation; aligning the useful unmapped reads to a junction library, to obtain a fused gene supported by the useful unmapped reads; calculating and gathering the fused sequence supported by the useful unmapped reads, to obtain information of the fused gene. And a system for detecting fusion transcripts is also provided.

9. 发明申请

US20110295784A1 ERROR CORRECTING METHOD OF TEST SEQUENCE, CORRESPONDING SYSTEM AND GENE ASSEMBLY EQUIPMENT 有权
标题翻译：测试顺序错误校正方法，相应系统和基因组装设备
公开(公告)号：US20110295784A1
公开(公告)日：2011-12-01
申请号：US13132038
申请日：2009-12-11
申请人： Jun Wang , Huanming Yang , Jian Wang
发明人： Jun Wang , Huanming Yang , Jian Wang
IPC分类号： G06N3/12
CPC分类号： G06F19/24 , C12Q1/6874 , G06F19/22
摘要： The present invention provides an error correcting method of test sequence, which involves receiving test sequences, configuring high frequency short string list based on a preset high frequency threshold value, traversing each received test sequence, searching an area with the largest number of continuous high frequency short strings on each test sequence in combination with high frequency short string list, configuring whole left sequence and/or right sequence of high frequency short strings at left side and/or right side of searched area according to corresponding received test sequence and high frequency short string list, and constituting corresponding test sequence according to configured left and/or right sequence and searched area. The present invention also provides corresponding error correcting system of test sequence and gene assembly equipment.
摘要翻译：本发明提供一种测试序列的纠错方法，其包括接收测试序列，基于预设的高频阈值配置高频短串列表，遍历每个接收的测试序列，搜索具有最大数目的连续高频区域每个测试序列上的短串组合高频短串列表，根据相应的接收测试序列和高频短信配置搜索区域的左侧和/或右侧的全部左序列和/或右序列的高频短串字符串列表，并根据配置的左和/或右序列和搜索区域构成对应的测试序列。本发明还提供了相应的测试序列和基因组装设备的纠错系统。

10. 发明申请

US20150376697A1 METHOD AND SYSTEM TO DETERMINE BIOMARKERS RELATED TO ABNORMAL CONDITION 审中-公开
标题翻译：用于确定与异常条件相关的生物标志物的方法和系统
公开(公告)号：US20150376697A1
公开(公告)日：2015-12-31
申请号：US13640448
申请日：2012-08-22
申请人： Shenghui Li , Junjie Qin , Jianfeng Zhu , Dongya Zhang , Zhuye Jie , Jun Wang , Jian Wang , Huanming Yang
发明人： Shenghui Li , Junjie Qin , Jianfeng Zhu , Dongya Zhang , Zhuye Jie , Jun Wang , Jian Wang , Huanming Yang
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q2600/112
摘要： A method and system to determine biomarkers related to abnormal condition in a subject are provided, comprising:sequencing nucleic acid samples from a first and a second subject in order to obtain multiple sequences respectively consisting of the first and the second sequencing results, wherein the first subject is in the abnormal condition; and the second subject is not in the abnormal condition; and the nucleic acid samples from the first and the second subject are both isolated from the samples of the same type; and the first and the second subject belong to the same species; and determining the biomarkers related to the abnormal condition in the subject based on the difference between the first and the second sequencing results.
摘要翻译：提供了确定与受试者异常状况相关的生物标志物的方法和系统，其包括：对来自第一和第二受试者的核酸样品进行测序，以获得分别由第一和第二测序结果组成的多个序列，其中第一个受试者处于异常状况; 第二个受试者不处于异常状态; 并且来自第一和第二受试者的核酸样品均从相同类型的样品中分离; 第一和第二主题属于同一物种; 并且基于第一和第二测序结果之间的差异来确定与受试者的异常状况相关的生物标志物。

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