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1. 发明申请

US20110295977A1 BASE SEQUENCE CLUSTER GENERATING SYSTEM, BASE SEQUENCE CLUSTER GENERATING METHOD, PROGRAM FOR PERFORMING CLUSTER GENERATING METHOD, AND COMPUTER READABLE RECORDING MEDIUM ON WHICH PROGRAM IS RECORDED AND SYSTEM FOR PROVIDING BASE SEQUENCE INFORMATION 审中-公开
标题翻译：基本序列生成系统，基本序列集合生成方法，用于执行集群生成方法的程序和记录有程序的计算机可读记录介质以及用于提供基本序列信息的系统
公开(公告)号：US20110295977A1
公开(公告)日：2011-12-01
申请号：US13209097
申请日：2011-08-12
申请人： Tetsuo Shibuya
发明人： Tetsuo Shibuya
IPC分类号： G06F15/16 , G06F17/30
CPC分类号： G06F19/24 , G06F19/12 , G06F19/18 , G06F19/20 , G06F19/22
摘要： Provided is a base sequence cluster generating system, method, and program product for performing cluster generation. The base sequence cluster generating system utilizes a computer system having a database containing base sequences receives a query sequence over. The computer uses spliced base sequences as a query sequence to generate a first cluster including base sequences that are likely to constitute a spliced pair with the query sequence. Spliced alignment is applied to the generated first cluster to generate a second cluster including spliced pairs. The generated second cluster is returned to the requester.
摘要翻译：提供了用于执行集群生成的基本序列簇生成系统，方法和程序产品。基本序列簇生成系统利用具有包含基本序列的数据库的计算机系统接收查询序列。计算机使用拼接的碱基序列作为查询序列来生成包括可能构成与查询序列的拼接对的基序列的第一簇。拼接对齐被应用于所生成的第一簇以产生包括拼接对的第二簇。生成的第二个群集返回给请求者。

2. 发明授权

US07702595B2 Nucleotide sequence screening 失效
标题翻译：核苷酸序列筛选
公开(公告)号：US07702595B2
公开(公告)日：2010-04-20
申请号：US10783807
申请日：2004-02-20
申请人： Tetsuo Shibuya
发明人： Tetsuo Shibuya
IPC分类号： G06N3/12
CPC分类号： C40B30/02 , C12Q1/6813 , G06F19/20 , G06F19/22
摘要： A system for screening nucleotide sequences, a method therefor, a program, a recording medium, and a server on which the screening of nucleotide sequences is executed. The solution comprises a step of storing target nucleotide sequence data and a probe nucleotide sequence, a step of generating complementary sequence data from a probe nucleotide sequence that may be bound to the target nucleotide sequence, and storing a maximum acceptable edit distance between the target nucleotide sequence and the probe nucleotide sequence, a step of reading out each nucleotide sequence data and the maximum edit distance from each storing unit, and evaluating the binding possibility of the target nucleotide sequence data and the complementary sequence data in descending order of edit distance, and a step of storing the result of the binding evaluation in a storage unit.
摘要翻译：用于筛选核苷酸序列的系统，其方法，程序，记录介质和在其上执行核苷酸序列筛选的服务器。所述溶液包括存储靶核苷酸序列数据和探针核苷酸序列的步骤，从可能与靶核苷酸序列结合的探针核苷酸序列产生互补序列数据的步骤，以及存储目标核苷酸序列之间的最大可接受编辑距离序列和探针核苷酸序列，从每个存储单元读出每个核苷酸序列数据和最大编辑距离的步骤，以编辑距离的降序评估目标核苷酸序列数据和互补序列数据的结合可能性，以及将结合评估结果存储在存储单元中的步骤。

3. 发明申请

US20100057370A1 Nucleotide Sequence Screening 失效
标题翻译：核苷酸序列筛选
公开(公告)号：US20100057370A1
公开(公告)日：2010-03-04
申请号：US12541306
申请日：2009-08-14
申请人： Tetsuo Shibuya
发明人： Tetsuo Shibuya
IPC分类号： G06F19/00
CPC分类号： C40B30/02 , C12Q1/6813 , G06F19/20 , G06F19/22
摘要： A system for screening nucleotide sequences, a method therefor, a program, a recording medium, and a server on which the screening of nucleotide sequences is executed. The solution comprises a step of storing target nucleotide sequence data and a probe nucleotide sequence, a step of generating complementary sequence data from a probe nucleotide sequence that may be bound to the target nucleotide sequence, and storing a maximum acceptable edit distance between the target nucleotide sequence and the probe nucleotide sequence, a step of reading out each nucleotide sequence data and the maximum edit distance from each storing unit, and evaluating the binding possibility of the target nucleotide sequence data and the complementary sequence data in descending order of edit distance, and a step of storing the result of the binding evaluation in a storage unit.
摘要翻译：用于筛选核苷酸序列的系统，其方法，程序，记录介质和在其上执行核苷酸序列筛选的服务器。所述溶液包括存储靶核苷酸序列数据和探针核苷酸序列的步骤，从可能与靶核苷酸序列结合的探针核苷酸序列产生互补序列数据的步骤，以及存储目标核苷酸序列之间的最大可接受编辑距离序列和探针核苷酸序列，从每个存储单元读出每个核苷酸序列数据和最大编辑距离的步骤，以编辑距离的降序评估目标核苷酸序列数据和互补序列数据的结合可能性，以及将结合评估结果存储在存储单元中的步骤。

4. 发明授权

US08239141B2 Method for changing a target array, a method for analyzing a structure, and an apparatus, a storage medium and a transmission medium therefor 失效
标题翻译：用于改变目标阵列的方法，用于分析结构的方法，以及装置，存储介质及其传输介质
公开(公告)号：US08239141B2
公开(公告)日：2012-08-07
申请号：US11536102
申请日：2006-09-28
申请人： Tetsuo Shibuya
发明人： Tetsuo Shibuya
IPC分类号： G01N33/48
CPC分类号： G06F19/28 , G06F19/22
摘要： The objective of the present invention is the efficient analyzation of the structure of an array.By performing the prev(S) calculation for a character string S, if in the character string S a like variable is present upstream of a second variable, the second variable is changed to a numerical value that indicates the distance to the upstream like variable. But if in the character string S a like variable is not present upstream of a variable, that variable is changed to “0” to obtain a character string S1. Further, by performing the compl(S) calculation for the a character string S, if in the character string S a complementary variable is present upstream of a second variable, the second variable is changed to a numerical value that indicates the distance to the complementary variable. But if in the character string S a complementary variable is not present upstream of a variable, that variable is changed to “0” to obtain a character string S2 (102). A single suffix tree (structure suffix tree) is generated by regarding the character strings S1 and S2 as a pair of corresponding character strings (104 to 114), and the obtained structure suffix tree is employed to analyze the structure of the array that is represented by the character string S.
摘要翻译：本发明的目的是有效地分析阵列的结构。通过对字符串S进行prev（S）的计算，如果在字符串S中存在类似的变量，则在第二变量的上游存在，则将第二变量变更为表示与上游类似变量的距离的数值。但是，如果在字符串S中，在变量的上游不存在类似的变量，则该变量变为“0”以获得字符串S1。此外，通过对字符串S进行compl（S）计算，如果在字符串S中存在互补变量存在于第二变量的上游，则将第二变量变更为表示到互补的距离的数值变量。但是，如果字符串S中的变量不存在互补变量，那么该变量变为“0”以获得字符串S2（102）。通过将字符串S1和S2作为一对相应的字符串（104至114）来生成单个后缀树（结构后缀树），并且使用所获得的结构后缀树来分析表示的数组的结构由字符串S.

5. 发明授权

US07561974B2 System and method for identifying genes 失效
公开(公告)号：US07561974B2
公开(公告)日：2009-07-14
申请号：US10059421
申请日：2002-01-31
申请人： Tetsuo Shibuya , Isidore Rigoutsos
发明人： Tetsuo Shibuya , Isidore Rigoutsos
IPC分类号： G01N33/48
CPC分类号： G06F19/22
摘要： A system and method for identifying genes that employs a pattern database, an input device for inputting a DNA sequence, and a processor for processing the DNA sequence and patterns to identify a putative gene. The processor may determine open reading frames (ORFs) in the DNA sequence, generate an amino acid translation for each ORF, and identify a match of a pattern in the amino acid translation.

6. 发明申请

US20050112670A1 Chromosome state analysis 有权
标题翻译：染色体状态分析
公开(公告)号：US20050112670A1
公开(公告)日：2005-05-26
申请号：US10983405
申请日：2004-11-08
申请人： Makoto Kano , Tetsuo Shibuya
发明人： Makoto Kano , Tetsuo Shibuya
IPC分类号： C12N15/09 , C12M1/00 , C12Q1/68 , G01N33/48 , G01N33/50 , G06F17/18 , G06F19/00 , G06F19/18 , G06F19/20
CPC分类号： G06F19/20
摘要： Analyzes chromosomal states based on amounts of expression of genes. An example apparatus comprising: a unit for storing probability distribution of amounts of expression of genes for each chromosomal state, assuming any of the chromosomal states in which the distributions of amounts of expression are different; a unit for supplying state transition probability indicating probability in which when each of the genes arrayed on the chromosome assumes any one of the chromosomal states, a certain gene array assumes any one of the chromosomal states; an input unit for receiving an expression amount measurement value of the amount of expression for each of the genes on the chromosome; and a unit for detecting a combination of the chromosomal states maximizing a probability among those that can be assumed by the genes on the chromosome, based on the probability distribution and the state transition probability.
摘要翻译：基于基因表达量分析染色体状态。一种示例性装置，包括：假设任何一种表达量分布不同的染色体状态，存储每种染色体状态的基因表达量概率分布的单元; 提供状态转移概率的单位，其指示当染色体上排列的每个基因呈现染色体状态中的任一种时的概率，某个基因阵列呈现染色体状态中的任何一种; 用于接收染色体上每个基因的表达量的表达量测量值的输入单元; 以及用于检测染色体状态的组合的单元，其基于概率分布和状态转移概率来检测可以由染色体上的基因假定的染色体状态之间的概率最大化。

7. 发明授权

US06356911B1 Shortest path search system 失效
标题翻译：最短路径搜索系统
公开(公告)号：US06356911B1
公开(公告)日：2002-03-12
申请号：US09210325
申请日：1998-12-11
申请人： Tetsuo Shibuya
发明人： Tetsuo Shibuya
IPC分类号： G06F1700
CPC分类号： G01C21/3446 , G06F17/509 , Y10S707/99933 , Y10S707/99934 , Y10S707/99935 , Y10S707/99936 , Y10S707/99942
摘要： An efficient method and system is provided for searching for the shortest paths between a source and multiple destinations, and between multiple sources and multiple destinations. The speed of the conventional Dijkstra method, which is the basic calculation method, is increased by employing information concerning the relationship between a node and a set of destinations on a graph. The relationship information is constituted by the estimate function h(v) concerning a specific node v and a set T of destinations, where h(v) is a lower bound of all the shortest path lengths extending from node v to each of the destination sets T. Employment of the estimate function can increase the speed of the Dijkstra method.
摘要翻译：提供了一种有效的方法和系统，用于搜索源与多个目的地之间，以及多个源和多个目的地之间的最短路径。通过使用关于图上的节点和一组目的地之间的关系的信息来增加作为基本计算方法的常规Dijkstra方法的速度。关系信息由关于特定节点v和目的地集合T的估计函数h（v）构成，其中h（v）是从节点v延伸到每个目的地集合的所有最短路径长度的下限使用估计函数可以提高Dijkstra方法的速度。

8. 发明授权

US09589102B2 Base sequence cluster generating system, base sequence cluster generating method, program for performing cluster generating method, and computer readable recording medium on which program is recorded and system for providing base sequence information 有权
标题翻译：基本序列簇生成系统，基本序列簇生成方法，用于执行簇生成方法的程序和记录有程序的计算机可读记录介质以及用于提供基本序列信息的系统
公开(公告)号：US09589102B2
公开(公告)日：2017-03-07
申请号：US13209097
申请日：2011-08-12
申请人： Tetsuo Shibuya
发明人： Tetsuo Shibuya
IPC分类号： G01N33/48 , G01N33/50 , G06F19/24 , G06F19/18 , G06F19/20 , G06F19/12 , G06F19/22
CPC分类号： G06F19/24 , G06F19/12 , G06F19/18 , G06F19/20 , G06F19/22
摘要： Provided is a base sequence cluster generating system, method, and program product for performing cluster generation. The base sequence cluster generating system utilizes a computer system having a database containing base sequences receives a query sequence over. The computer uses spliced base sequences as a query sequence to generate a first cluster including base sequences that are likely to constitute a spliced pair with the query sequence. Spliced alignment is applied to the generated first cluster to generate a second cluster including spliced pairs. The generated second cluster is returned to the requester.
摘要翻译：提供了用于执行集群生成的基本序列簇生成系统，方法和程序产品。基本序列簇生成系统利用具有包含基本序列的数据库的计算机系统接收查询序列。计算机使用拼接的碱基序列作为查询序列来生成包括可能构成与查询序列的拼接对的基序列的第一簇。拼接对齐被应用于所生成的第一簇以产生包括拼接对的第二簇。生成的第二个群集返回给请求者。

9. 发明授权

US08594940B2 System and method for analyzing chromosomal states based on gene expression 有权
标题翻译：基于基因表达分析染色体状态的系统和方法
公开(公告)号：US08594940B2
公开(公告)日：2013-11-26
申请号：US10983405
申请日：2004-11-08
申请人： Makoto Kano , Tetsuo Shibuya
发明人： Makoto Kano , Tetsuo Shibuya
IPC分类号： G01N33/48
CPC分类号： G06F19/20
摘要： Analyzes chromosomal states based on amounts of expression of genes. An example apparatus comprising: a unit for storing probability distribution of amounts of expression of genes for each chromosomal state, assuming any of the chromosomal states in which the distributions of amounts of expression are different; a unit for supplying state transition probability indicating probability in which when each of the genes arrayed on the chromosome assumes any one of the chromosomal states, a certain gene array assumes any one of the chromosomal states; an input unit for receiving an expression amount measurement value of the amount of expression for each of the genes on the chromosome; and a unit for detecting a combination of the chromosomal states maximizing a probability among those that can be assumed by the genes on the chromosome, based on the probability distribution and the state transition probability.
摘要翻译：基于基因表达量分析染色体状态。一种示例性装置，包括：假设任何一种表达量分布不同的染色体状态，存储每种染色体状态的基因表达量概率分布的单元; 提供状态转移概率的单位，其指示当染色体上排列的每个基因呈现染色体状态中的任一种时的概率，某个基因阵列呈现染色体状态中的任何一种; 用于接收染色体上每个基因的表达量的表达量测量值的输入单元; 以及用于检测染色体状态的组合的单元，其基于概率分布和状态转移概率来检测可以由染色体上的基因假定的染色体状态之间的概率最大化。

10. 发明授权

US07877336B2 Nucleotide sequence screening 失效
标题翻译：核苷酸序列筛选
公开(公告)号：US07877336B2
公开(公告)日：2011-01-25
申请号：US12541306
申请日：2009-08-14
申请人： Tetsuo Shibuya
发明人： Tetsuo Shibuya
IPC分类号： G06N3/12
CPC分类号： C40B30/02 , C12Q1/6813 , G06F19/20 , G06F19/22
摘要： A system for screening nucleotide sequences, a method therefor, a program, a recording medium, and a server on which the screening of nucleotide sequences is executed. The solution comprises a step of storing target nucleotide sequence data and a probe nucleotide sequence, a step of generating complementary sequence data from a probe nucleotide sequence that may be bound to the target nucleotide sequence, and storing a maximum acceptable edit distance between the target nucleotide sequence and the probe nucleotide sequence, a step of reading out each nucleotide sequence data and the maximum edit distance from each storing unit, and evaluating the binding possibility of the target nucleotide sequence data and the complementary sequence data in descending order of edit distance, and a step of storing the result of the binding evaluation in a storage unit.
摘要翻译：用于筛选核苷酸序列的系统，其方法，程序，记录介质和在其上执行核苷酸序列筛选的服务器。所述溶液包括存储靶核苷酸序列数据和探针核苷酸序列的步骤，从可能与靶核苷酸序列结合的探针核苷酸序列产生互补序列数据的步骤，以及存储目标核苷酸序列之间的最大可接受编辑距离序列和探针核苷酸序列，从每个存储单元读出每个核苷酸序列数据和最大编辑距离的步骤，以编辑距离的降序评估目标核苷酸序列数据和互补序列数据的结合可能性，以及将结合评估结果存储在存储单元中的步骤。

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