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1. 发明申请

US20120016595A1 TRANSCRIPT MAPPING METHOD 失效
标题翻译：转录映射方法
公开(公告)号：US20120016595A1
公开(公告)日：2012-01-19
申请号：US13183712
申请日：2011-07-15
申请人： Wing Kin Ken SUNG , Yijun RUAN
发明人： Wing Kin Ken SUNG , Yijun RUAN
IPC分类号： G06F19/18
CPC分类号： G06F19/18 , G06F19/22
摘要： A transcript mapping method according to an embodiment of the invention is described hereinafter and combines short tag based (SAGE and MPSS) efficiency with the accuracy of full-length cDNA (flcDNA) for comprehensive characterization of transcriptomes. This method is also referred to as Gene Identification Signature (GIS) analysis. In this method, the 5′ and 3′ ends of full-length cDNA clones are initially extracted into a ditag structure, with the ditag concatemers of the ditag being subsequently sequenced in an efficient manner, and finally mapped to the genome for defining the gene structure. As a GIS ditag represents the 5′ and 3′ ends of a transcript, it is more informative than SAGE and MPSS tags. Segment lengths between 5′ and 3′ tag pairs are obtainable including orientation, ordering and chromosome family for efficient transcript mapping and gene location identification. Furthermore, a compressed suffix array (CSA) is used for indexing the genome sequence for improve mapping speed and to reduce computational memory requirements.
摘要翻译：下文描述了根据本发明实施方案的转录本映射方法，并将基于短标签（SAGE和MPSS）的效率与全长cDNA（flcDNA）的准确度相结合，用于全面表征转录组。这种方法也被称为基因识别签名（GIS）分析。在该方法中，全长cDNA克隆的5'和3'末端最初被提取到ditag结构中，ditag的ditag连接体随后以有效的方式进行测序，最后映射到用于定义基因的基因组结构体。作为一个地理信息系统地图代表了抄本的5'和3'端，它比SAGE和MPSS标签更具信息。可以获得5'和3'标签对之间的片段长度，包括定向，排列和染色体家族，用于有效的转录映射和基因位置识别。此外，压缩后缀阵列（CSA）用于索引基因组序列以提高映射速度并减少计算存储器要求。

2. 发明申请

US20070238101A1 Nucleic acid interaction analysis 有权
标题翻译：核酸相互作用分析
公开(公告)号：US20070238101A1
公开(公告)日：2007-10-11
申请号：US11373519
申请日：2006-03-13
申请人： Yijun Ruan , Melissa Fullwood , Chia Wei , Huck Ng
发明人： Yijun Ruan , Melissa Fullwood , Chia Wei , Huck Ng
IPC分类号： C12Q1/68 , C12P19/34 , C07H21/04
CPC分类号： C12N15/1065 , C12Q1/6804 , C12Q2525/197 , C12Q2525/131 , C12Q2521/313 , C12Q2531/113 , C12Q2525/191 , C12Q2523/101
摘要： The present invention provides an isolated oligonucleotide and a method using the isolated oligonucleotide to detect and/or identify at least two polynucleotides from a nucleic acid-protein complex. The oligonucleotide comprises at least one first tag and at least one second tag, wherein the first and second tags are obtained from a nucleic acid-protein complex.
摘要翻译：本发明提供分离的寡核苷酸和使用分离的寡核苷酸从核酸 - 蛋白复合物检测和/或鉴定至少两种多核苷酸的方法。寡核苷酸包含至少一个第一标签和至少一个第二标签，其中第一个和第二个标签是从核酸 - 蛋白质复合物获得的。

3. 发明授权

US08428882B2 Method of processing and/or genome mapping of diTag sequences 失效
标题翻译： diTag序列的处理和/或基因组图谱的方法
公开(公告)号：US08428882B2
公开(公告)日：2013-04-23
申请号：US11151591
申请日：2005-06-14
申请人： Kuo Ping Chiu , Yijun Ruan , Chia Lin Wei
发明人： Kuo Ping Chiu , Yijun Ruan , Chia Lin Wei
IPC分类号： G01N33/50
CPC分类号： G06F19/28 , G06F19/22
摘要： There is provided a method and system for processing and/or mapping ditag nucleotide sequence(s) to a genome, the ditag sequence comprising the 5′ terminal tag and the 3′ terminal tag of a nucleic acid molecule or fragment thereof or genomic fragment. The method of processing comprises preparing a database or file comprising at least one ditag sequence. The method of mapping comprises preparing a database or file of ditag(s), and mapping the ditag sequence(s) to the genome, comprising matching the 5′ and the 3′ terminal tags of the ditag sequence to at least a portion of the genome.
摘要翻译：提供了用于处理和/或将基因组的核苷酸序列映射到基因组的方法和系统，包括核酸分子或其片段的5'末端标签和3'末端标签的基因组序列或基因组片段。所述处理方法包括准备包含至少一个ditag序列的数据库或文件。映射方法包括准备数据库或文件的一个或多个ditag序列，并将该ditag序列映射到基因组，包括将ditag序列的5'和3'末端标签与至少一部分基因组

4. 发明授权

US08222005B2 Method for gene identification signature (GIS) analysis 有权
标题翻译：基因鉴别特征（GIS）分析方法
公开(公告)号：US08222005B2
公开(公告)日：2012-07-17
申请号：US10664234
申请日：2003-09-17
申请人： Yijun Ruan , Patrick Ng , Chialin Wei
发明人： Yijun Ruan , Patrick Ng , Chialin Wei
IPC分类号： C12P19/34 , C12N15/66 , G01N33/50
CPC分类号： C12Q1/6809 , C12N15/1065 , C12N15/1093 , C12N15/1096 , C12Q1/6855 , C12Q2525/191 , C12Q2525/131 , C12Q2521/313
摘要： An isolated oligonucleotide comprising at least one ditag, wherein the ditag comprises two joined first and second sequence tags, wherein the first tag comprises the 5′-terminus sequence and the second tag comprises the 3′-terminus sequence of a nucleic acid molecule or a fragment thereof. The ditag analysis is useful for gene discovery and genome mapping.
摘要翻译：包含至少一个ditag的分离的寡核苷酸，其中所述ditag包含两个连接的第一和第二序列标签，其中所述第一标签包含5'-末端序列，并且所述第二标签包含核酸分子的3'-末端序列或片段。 ditag分析可用于基因发现和基因组图谱。

5. 发明申请

US20080124707A1 Nucleic acid concatenation 审中-公开
标题翻译：核酸连接
公开(公告)号：US20080124707A1
公开(公告)日：2008-05-29
申请号：US11449872
申请日：2006-06-09
申请人： Yijun Ruan , Patrick Ng , Melissa Jane Fullwood , Yen Ling Lee
发明人： Yijun Ruan , Patrick Ng , Melissa Jane Fullwood , Yen Ling Lee
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6804 , C12Q1/6809 , C12Q2525/151 , C12Q2525/131 , C12Q2539/103
摘要： The present invention provides a method of manipulating nucleic acids. In particular, of length-controlled concatenating of nucleotide fragments, the method comprising: (a) providing at least two nucleotide fragments, wherein each fragment has one ligatable end and one non-ligatable end; and (b) allowing the two fragments to ligate at the ligatable ends to form an oligonucleotide comprising at least two concatenated nucleotide fragments. The present invention also provides an isolated oligonucleotide comprising at least two nucleotide fragments, wherein each fragment has at least one ligatable end and and one non-ligatable end, and the fragments are ligated at the ligatable ends to form the oligonucleotide.
摘要翻译：本发明提供了一种操纵核酸的方法。特别地，长度控制的核苷酸片段连接，所述方法包括：（a）提供至少两个核苷酸片段，其中每个片段具有一个可连接末端和一个不可连接末端; 和（b）允许两个片段在可连接的末端连接以形成包含至少两个连接的核苷酸片段的寡核苷酸。本发明还提供了包含至少两个核苷酸片段的分离的寡核苷酸，其中每个片段具有至少一个可连接的末端和一个不可连接的末端，并且将片段连接在可连接的末端以形成寡核苷酸。

6. 发明申请

US20080104729A1 Nucleic acid molecules and other molecules associated with plants 审中-公开
标题翻译：核酸分子和与植物相关的其他分子
公开(公告)号：US20080104729A1
公开(公告)日：2008-05-01
申请号：US11976388
申请日：2007-10-24
申请人： Timothy Conner , Yijun Ruan
发明人： Timothy Conner , Yijun Ruan
IPC分类号： A01H1/00 , A01H5/00 , C07H21/04 , C12N15/87
CPC分类号： C07K14/415
摘要： Expressed Sequence Tags (ESTs) isolated from Arabidopsis thaliana are disclosed. The ESTs provide a unique molecular tool for the targeting and isolation of novel genes for plant protection and improvement. The disclosed ESTs have utility in the development of new strategies for understanding critical plant developmental and metabolic pathways. The disclosed ESTs have particular utility in isolating genes and promoters, identifying and mapping the genes involved in developmental and metabolic pathways, and determining gene function. Sequence homology analyses using the ESTs provided in the present invention, will result in more efficient gene screening for desirable agronomic traits. An expanding database of these select pieces of the plant genomics puzzle will quickly expand the knowledge necessary for subsequent functional validation, a key limitation in current plant biotechnology efforts.
摘要翻译：公开了从拟南芥分离的表达序列标签（ESTs）。 EST为靶基因和分离新基因提供了独特的分子工具，用于植物保护和改良。所公开的EST可用于开发用于了解关键植物发育和代谢途径的新策略。所公开的EST在分离基因和启动子方面具有特别的用途，鉴定和绘制参与发育和代谢途径的基因以及确定基因功能。使用本发明提供的EST的序列同源性分析将导致对所需农学性状的更有效的基因筛选。这些植物基因组学难题的这些精选片段的不断扩展的数据库将快速扩展后续功能验证所必需的知识，这是当前植物生物技术努力的关键限制。

7. 发明申请

US20060084083A1 Method to generate or determine nucleic acid tags corresponding to the terminal ends of DNA molecules using sequences analysis of gene expression (terminal SAGE) 有权
标题翻译：使用基因表达序列分析（终端SAGE）产生或确定对应于DNA分子末端的核酸标签的方法
公开(公告)号：US20060084083A1
公开(公告)日：2006-04-20
申请号：US11145005
申请日：2005-06-03
申请人： Yijun Ruan , Chialin Wei
发明人： Yijun Ruan , Chialin Wei
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6809 , C12Q2539/103
摘要： A method of providing an indication of an instance of expression of a gene is described herein, the method which may comprise the steps of: (a) providing a complementary deoxyribonucleic acid (cDNA) having a terminus comprising a terminal transcribed sequence of a gene; (b) linking the cDNA to an linker sequence thereby forming a linked nucleic acid, in which the linker sequence comprises a first recognition site for a first nucleic acid cleavage enzyme, preferably a restriction endonuclease, that allows nucleic acid cleavage at a site distant from the first recognition site; and (c) cleaving the linked nucleic acid with the first nucleic acid cleavage enzyme to provide a linked tag, in which the linked tag comprises a nucleotide sequence tag representative of a terminal transcribed sequence of the gene; and (d) detecting the presence or identity of the linked tag or the nucleotide sequence tag to provide an indication of an instance of gene expression.
摘要翻译：本文描述了提供基因表达实例的指示的方法，所述方法可以包括以下步骤：（a）提供具有包含基因的末端转录序列的末端的互补脱氧核糖核酸（cDNA）（b）将cDNA连接到接头序列，从而形成连接的核酸，其中接头序列包含用于第一核酸切割酶的第一识别位点，优选限制性内切核酸酶，其允许在远离的位点进行核酸切割第一个认可网站; 和（c）用第一核酸切割酶切割连接的核酸以提供连接的标签，其中连接的标签包含代表该基因的末端转录序列的核苷酸序列标签; 和（d）检测连锁标签或核苷酸序列标签的存在或身份以提供基因表达实例的指示。

8. 发明授权

US08762073B2 Transcript mapping method 失效
标题翻译：记录映射方法
公开(公告)号：US08762073B2
公开(公告)日：2014-06-24
申请号：US13183712
申请日：2011-07-15
申请人： Wing Kin Ken Sung , Yijun Ruan
发明人： Wing Kin Ken Sung , Yijun Ruan
IPC分类号： G01N33/50
CPC分类号： G06F19/18 , G06F19/22
摘要： A transcript mapping method according to an embodiment of the invention is described hereinafter and combines short tag based (SAGE and MPSS) efficiency with the accuracy of full-length cDNA (flcDNA) for comprehensive characterization of transcriptomes. This method is also referred to as Gene Identification Signature (GIS) analysis. In this method, the 5′ and 3′ ends of full-length cDNA clones are initially extracted into a ditag structure, with the ditag concatemers of the ditag being subsequently sequenced in an efficient manner, and finally mapped to the genome for defining the gene structure. As a GIS ditag represents the 5′ and 3′ ends of a transcript, it is more informative than SAGE and MPSS tags. Segment lengths between 5′ and 3′ tag pairs are obtainable including orientation, ordering and chromosome family for efficient transcript mapping and gene location identification. Furthermore, a compressed suffix array (CSA) is used for indexing the genome sequence for improve mapping speed and to reduce computational memory requirements.
摘要翻译：下文描述了根据本发明实施方案的转录本映射方法，并将基于短标签（SAGE和MPSS）的效率与全长cDNA（flcDNA）的准确度相结合，用于全面表征转录组。这种方法也被称为基因识别签名（GIS）分析。在该方法中，全长cDNA克隆的5'和3'末端最初被提取到ditag结构中，ditag的ditag连接体随后以有效的方式进行测序，最后映射到用于定义基因的基因组结构体。作为一个地理信息系统地图代表了抄本的5'和3'端，它比SAGE和MPSS标签更具信息。可以获得5'和3'标签对之间的片段长度，包括定向，排列和染色体家族，用于有效的转录映射和基因位置识别。此外，压缩后缀阵列（CSA）用于索引基因组序列以提高映射速度并减少计算存储器要求。

9. 发明申请

US20120214157A1 METHOD TO GENERATE OR DETERMINE NUCLEIC ACID TAGS CORRESPONDING TO THE TERMINAL ENDS OF DNA MOLECULES USING SEQUENCES ANALYSIS OF GENE EXPRESSION (TERMINAL SAGE) 审中-公开
标题翻译：使用序列分析基因表达（终端信号）生成或确定与DNA分子末端相关的核酸标签的方法
公开(公告)号：US20120214157A1
公开(公告)日：2012-08-23
申请号：US13407792
申请日：2012-02-29
申请人： Yijun Ruan , Chialin Wei
发明人： Yijun Ruan , Chialin Wei
IPC分类号： C12Q1/68 , G06F19/28
CPC分类号： C12Q1/6809 , C12Q2539/103
摘要： We describe a method of providing an indication of an instance of expression of a gene, the method comprising the steps of: (a) providing a complementary deoxyribonucleic acid (cDNA) having a terminus comprising a terminal transcribed sequence of a gene; (b) linking the cDNA to an linker sequence thereby forming a linked nucleic acid, in which the linker sequence comprises a first recognition site for a first nucleic acid cleavage enzyme, preferably a restriction endonuclease, that allows nucleic acid cleavage at a site distant from the first recognition site; and (c) cleaving the linked nucleic acid with the first nucleic acid cleavage enzyme to provide a linked tag, in which the linked tag comprises a nucleotide sequence tag representative of a terminal transcribed sequence of the gene; and (d) detecting the presence or identity of the linked tag or the nucleotide sequence tag to provide an indication of an instance of gene expression.
摘要翻译：我们描述了提供基因表达实例的指示的方法，所述方法包括以下步骤：（a）提供具有包含基因的末端转录序列的末端的互补脱氧核糖核酸（cDNA）（b）将cDNA连接到接头序列，从而形成连接的核酸，其中接头序列包含用于第一核酸切割酶的第一识别位点，优选限制性内切核酸酶，其允许在远离的位点进行核酸切割第一个认可网站; 和（c）用第一核酸切割酶切割连接的核酸以提供连接的标签，其中连接的标签包含代表该基因的末端转录序列的核苷酸序列标签; 和（d）检测连锁标签或核苷酸序列标签的存在或身份以提供基因表达实例的指示。

10. 发明授权

US08158355B2 Method to generate or determine nucleic acid tags corresponding to the terminal ends of DNA molecules using sequences analysis of gene expression (terminal SAGE) 有权
标题翻译：使用基因表达序列分析（终端SAGE）产生或确定对应于DNA分子末端的核酸标签的方法
公开(公告)号：US08158355B2
公开(公告)日：2012-04-17
申请号：US11145005
申请日：2005-06-03
申请人： Yijun Ruan , Chialin Wei
发明人： Yijun Ruan , Chialin Wei
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6809 , C12Q2539/103
摘要： A method of providing an indication of an instance of expression of a gene is described herein, the method which may comprise the steps of: (a) providing a complementary deoxyribonucleic acid (cDNA) having a terminus comprising a terminal transcribed sequence of a gene; (b) linking the cDNA to an linker sequence thereby forming a linked nucleic acid, in which the linker sequence comprises a first recognition site for a first nucleic acid cleavage enzyme, preferably a restriction endonuclease, that allows nucleic acid cleavage at a site distant from the first recognition site; and (c) cleaving the linked nucleic acid with the first nucleic acid cleavage enzyme to provide a linked tag, in which the linked tag comprises a nucleotide sequence tag representative of a terminal transcribed sequence of the gene; and (d) detecting the presence or identity of the linked tag or the nucleotide sequence tag to provide an indication of an instance of gene expression.
摘要翻译：本文描述了提供基因表达实例的指示的方法，所述方法可以包括以下步骤：（a）提供具有包含基因的末端转录序列的末端的互补脱氧核糖核酸（cDNA）（b）将cDNA连接到接头序列，从而形成连接的核酸，其中接头序列包含用于第一核酸切割酶的第一识别位点，优选限制性内切核酸酶，其允许在远离的位点进行核酸切割第一个认可网站; 和（c）用第一核酸切割酶切割连接的核酸以提供连接的标签，其中连接的标签包含代表该基因的末端转录序列的核苷酸序列标签; 和（d）检测连锁标签或核苷酸序列标签的存在或身份以提供基因表达实例的指示。

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