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1. 发明授权

US09390163B2 Method, system and software arrangement for detecting or determining similarity regions between datasets 有权
标题翻译：用于检测或确定数据集之间的相似区域的方法，系统和软件布置
公开(公告)号：US09390163B2
公开(公告)日：2016-07-12
申请号：US11410692
申请日：2006-04-24
申请人： Salvatore Paxia , Bhubaneswar Mishra , Yi Zhou
发明人： Salvatore Paxia , Bhubaneswar Mishra , Yi Zhou
IPC分类号： G01N33/48 , G01N33/50 , G06F17/30 , G06F19/12 , G06F19/24 , G06F19/26 , G06F19/22
CPC分类号： G06F17/30675 , G06F19/12 , G06F19/22 , G06F19/24 , G06F19/26
摘要： Methods, systems, and computer-readable media are provided which can identify and provide local variations in regions of similarity among two or more data sets. These data sets may be represented as sequences such as, e.g., genomic sequences or words in a text. The local variations in similarity levels can be provided by selecting an initial prior distribution relating the data sets, organizing the first data set into windows and the remaining data sets into blocks, using the priors to sample one or more sets of words from the first data set, computing a similarity curve from exact and inexact matches for these words and, if convergence of results is not achieved, computing a new set of priors and repeating the sampling and computation of similarity curves. The computations can be performed using an amount of computational time that is linearly proportional to the size of the data sets.
摘要翻译：提供了可以识别和提供两个或多个数据集之间的相似区域中的局部变化的方法，系统和计算机可读介质。这些数据集可以表示为例如文本中的基因组序列或单词的序列。相似度级别的局部变化可以通过选择与数据集相关联的初始先验分布，将第一数据集合组合成窗口并将剩余的数据集组织成块来提供，使用先验从第一数据中采样一个或多个单词组设置，从这些词的精确和不精确匹配计算相似曲线，并且如果没有实现结果的收敛，则计算新的先验集合并重复相似曲线的采样和计算。可以使用与数据集的大小成线性比例的计算时间量来执行计算。

2. 发明申请

US20080046187A1 Method, system and software arrangement for detecting or determining similarity regions between datasets 有权
标题翻译：用于检测或确定数据集之间的相似区域的方法，系统和软件布置
公开(公告)号：US20080046187A1
公开(公告)日：2008-02-21
申请号：US11410692
申请日：2006-04-24
申请人： Salvatore Paxia , Bhubaneswar Mishra , Yi Zhou
发明人： Salvatore Paxia , Bhubaneswar Mishra , Yi Zhou
IPC分类号： G06F19/00
CPC分类号： G06F17/30675 , G06F19/12 , G06F19/22 , G06F19/24 , G06F19/26
摘要： Methods, systems, and computer-readable media are provided which can identify and provide local variations in regions of similarity among two or more data sets. These data sets may be represented as sequences such as, e.g., genomic sequences or words in a text. The local variations in similarity levels can be provided by selecting an initial prior distribution relating the data sets, organizing the first data set into windows and the remaining data sets into blocks, using the priors to sample one or more sets of words from the first data set, computing a similarity curve from exact and inexact matches for these words and, if convergence of results is not achieved, computing a new set of priors and repeating the sampling and computation of similarity curves. The computations can be performed using an amount of computational time that is linearly proportional to the size of the data sets. The exemplary embodiments of the present invention can use Bayesian estimators to determine local variations in similarity levels and to refine estimates of the probabilistic distributions between iterations.
摘要翻译：提供了可以识别和提供两个或多个数据集之间的相似区域中的局部变化的方法，系统和计算机可读介质。这些数据集可以表示为例如文本中的基因组序列或单词的序列。相似度级别的局部变化可以通过选择与数据集相关联的初始先验分布，将第一数据集合组合成窗口并将剩余的数据集组织成块来提供，使用先验从第一数据中采样一个或多个单词组设置，从这些词的精确和不精确匹配计算相似曲线，并且如果没有实现结果的收敛，则计算新的先验集合并重复相似曲线的采样和计算。可以使用与数据集的大小成线性比例的计算时间量来执行计算。本发明的示例性实施例可以使用贝叶斯估计器来确定相似度级别中的局部变化并且改进迭代之间的概率分布的估计。

3. 发明申请

US20060155483A1 System and process for validating, aligning and reordering one or more genetic sequence maps using at least one ordered restriction map 有权
标题翻译：使用至少一个有序限制图来验证，对准和重新排序一个或多个遗传序列图的系统和过程
公开(公告)号：US20060155483A1
公开(公告)日：2006-07-13
申请号：US10432766
申请日：2001-09-28
申请人： Marco Antoniotti , Bhubaneswar Mishra , Thomas Anantharaman , Salvatore Paxia , David Schwartz
发明人： Marco Antoniotti , Bhubaneswar Mishra , Thomas Anantharaman , Salvatore Paxia , David Schwartz
IPC分类号： G06F19/00
CPC分类号： G06F19/22
摘要： A method and system are provided for comparing ordered segments of a first DNA restriction map with ordered segments of a second DNA restriction map to determine a level of accuracy the first DNA map and/or the second DNA map. In particular, the first and second DNA maps can be received (the first DNA map corresponding to a sequence DNA map, and the second DNA map corresponding to a genomic consensus DNA map as provided in an optical DNA map). Then, the accuracy of the first DNA map and/or the second DNA map is validated based on information associated with the first and second DNA maps. In addition, a method and system are provided for aligning a plurality of DNA sequences with a ordered DNA restriction map. The DNA sequences and the DNA map are received (the DNA sequences being fragments of a genome and the DNA map corresponding to a genomic consensus DNA map which relates to an optical ordered DNA map). Then, a level of accuracy of the DNA sequences and the DNA map is obtained based on information associated with the DNA sequences and the DNA map by means of the method and system described above. The locations of the DNA map at which the DNA sequences are capable of being associated with particular segments of the DNA map are located. Furthermore, it is possible to obtain locations of the DNA map (without the validation) by locating an optimal one of the locations for each of the DNA sequences for each of the locations.
摘要翻译：提供了一种方法和系统，用于将第一DNA限制性图谱的有序区段与第二DNA限制图谱的有序区段进行比较，以确定第一DNA图谱和/或第二DNA图谱的准确度。特别地，可以接收第一个和第二个DNA图谱（对应于序列DNA图谱的第一个DNA图谱，和对应于光学DNA图谱中提供的基因组共有DNA图谱的第二个DNA图谱）。然后，基于与第一和第二DNA图相关联的信息来验证第一DNA图和/或第二DNA图的准确性。此外，提供了用于使多个DNA序列与有序DNA限制图对齐的方法和系统。接受DNA序列和DNA图谱（DNA序列是基因组的片段，DNA图谱对应于涉及光学有序DNA图谱的基因组共有DNA图谱）。然后，通过上述方法和系统，基于与DNA序列和DNA图谱相关的信息，获得DNA序列和DNA图谱的准确度。 DNA序列的DNA图谱位置可以与DNA图谱的特定片段相关联。此外，通过为每个位置定位每个DNA序列的最佳位置之一，可以获得DNA图谱的位置（无需验证）。

4. 发明授权

US07831392B2 System and process for validating, aligning and reordering one or more genetic sequence maps using at least one ordered restriction map 有权
标题翻译：使用至少一个有序限制图来验证，对准和重新排序一个或多个遗传序列图的系统和过程
公开(公告)号：US07831392B2
公开(公告)日：2010-11-09
申请号：US10432766
申请日：2001-09-28
申请人： Marco Antoniotti , Bhubaneswar Mishra , Thomas Anantharaman , Salvatore Paxia , David C. Schwartz
发明人： Marco Antoniotti , Bhubaneswar Mishra , Thomas Anantharaman , Salvatore Paxia , David C. Schwartz
IPC分类号： G01N33/48 , C12Q1/68
CPC分类号： G06F19/22
摘要： A method and system are provided for comparing ordered segments of a first DNA restriction map with ordered segments of a second DNA restriction map to determine a level of accuracy the first DNA map and/or the second DNA map. In particular, the first and second DNA maps can be received (the first DNA map corresponding to a sequence DNA map, and the second DNA map corresponding to a genomic consensus DNA map as provided in an optical DNA map). Then, the accuracy of the first DNA map and/or the second DNA map is validated based on information associated with the first and second DNA maps. In addition, a method and system are provided for aligning a plurality of DNA sequences with a ordered DNA restriction map. The DNA sequences and the DNA map are received (the DNA sequences being fragments of a genome and the DNA map corresponding to a genomic consensus DNA map which relates to an optical ordered DNA map). Then, a level of accuracy of the DNA sequences and the DNA map is obtained based on information associated with the DNA sequences and the DNA map by means of the method and system described above. The locations of the DNA map at which the DNA sequences are capable of being associated with particular segments of the DNA map are located. Furthermore, it is possible to obtain locations of the DNA map (without the validation) by locating an optimal one of the locations for each of the DNA sequences for each of the locations.
摘要翻译：提供了一种方法和系统，用于将第一DNA限制性图谱的有序区段与第二DNA限制图谱的有序区段进行比较，以确定第一DNA图谱和/或第二DNA图谱的准确度。特别地，可以接收第一个和第二个DNA图谱（对应于序列DNA图谱的第一个DNA图谱，和对应于光学DNA图谱中提供的基因组共有DNA图谱的第二个DNA图谱）。然后，基于与第一和第二DNA图相关联的信息来验证第一DNA图和/或第二DNA图的准确性。此外，提供了用于使多个DNA序列与有序DNA限制图对齐的方法和系统。接受DNA序列和DNA图谱（DNA序列是基因组的片段，DNA图谱对应于涉及光学有序DNA图谱的基因组共有DNA图谱）。然后，通过上述方法和系统，基于与DNA序列和DNA图谱相关的信息，获得DNA序列和DNA图谱的准确度。 DNA序列的DNA图谱位置可以与DNA图谱的特定片段相关联。此外，通过为每个位置定位每个DNA序列的最佳位置之一，可以获得DNA图谱的位置（无需验证）。

5. 发明授权

US07788043B2 Methods, software arrangements and systems for aligning sequences which utilizes non-affine gap penalty procedure 有权
标题翻译：方法，软件安排和用于对齐序列的系统，其利用非仿射间隙惩罚程序
公开(公告)号：US07788043B2
公开(公告)日：2010-08-31
申请号：US11300749
申请日：2005-12-14
申请人： Ofer Gill , Yi Zhou , Bhubaneswar Mishra
发明人： Ofer Gill , Yi Zhou , Bhubaneswar Mishra
IPC分类号： G06F19/00 , G06F15/00 , G11C17/00
CPC分类号： G06F19/22
摘要： Methods, software arrangements and systems are provided which can utilize an exemplary embodiment of a procedure which can enable an efficient alignment of DNA sequences using piecewise-linear gap penalties that closely approximate general and biologically meaningful gap-functions. Accordingly, an exemplary process, software arrangement and system can be provided for obtaining data associated with an alignment between at least two data strings having a plurality of positions in the data strings. For example, at least one characteristic of an alignment can be provided between the data strings using a particular function. The particular function is capable of evaluating gaps between the strings in the alignment based on a non-affine gap-penalty function. According to another exemplary embodiment of the present invention provides process, software arrangement and system for obtaining data associated with an alignment between at least two data strings having a plurality of positions in the data strings. In particular, the alignment which is approximately optimal in substantially all circumstance can be determined for a computation time that is proportional to products of lengths of the strings. For example, the alignment may be determined using space that is proportional to a sum of the lengths of the data strings.
摘要翻译：提供了方法，软件安排和系统，其可以利用程序的示例性实施方案，其可以使得能够使用紧密接近一般和生物学有意义的间隙功能的分段线性间隙罚分来有效地对齐DNA序列。因此，可以提供示例性的过程，软件配置和系统来获得与在数据串中具有多个位置的至少两个数据串之间的对准相关联的数据。例如，可以使用特定功能在数据串之间提供对准的至少一个特性。该特定功能能够基于非仿射间隙罚函数来评估对准中的串之间的间隙。根据本发明的另一示例性实施例，提供了用于获得与在数据串中具有多个位置的至少两个数据串之间的对准相关联的数据的过程，软件安排和系统。具体而言，可以在与弦的长度的乘积成比例的计算时间确定在基本上所有情况下近似最佳的对准。例如，可以使用与数据串的长度的和成比例的空间来确定对准。

6. 发明申请

US20060173631A1 Methods, software arrangements and systems for aligning sequences which utilizes non-affine gap penalty procedure 有权
标题翻译：方法，软件安排和用于对齐序列的系统，其利用非仿射间隙惩罚程序
公开(公告)号：US20060173631A1
公开(公告)日：2006-08-03
申请号：US11300749
申请日：2005-12-14
申请人： Ofer Gill , Yi Zhou , Bhubaneswar Mishra
发明人： Ofer Gill , Yi Zhou , Bhubaneswar Mishra
IPC分类号： G06F19/00
CPC分类号： G06F19/22
摘要： Methods, software arrangements and systems are provided which can utilize an exemplary embodiment of a procedure which can enable an efficient alignment of DNA sequences using piecewise-linear gap penalties that closely approximate general and biologically meaningful gap-functions. Accordingly, an exemplary process, software arrangement and system can be provided for obtaining data associated with an alignment between at least two data strings having a plurality of positions in the data strings. For example, at least one characteristic of an alignment can be provided between the data strings using a particular function. The particular function is capable of evaluating gaps between the strings in the alignment based on a non-affine gap-penalty function. According to another exemplary embodiment of the present invention provides process, software arrangement and system for obtaining data associated with an alignment between at least two data strings having a plurality of positions in the data strings. In particular, the alignment which is approximately optimal in substantially all circumstance can be determined for a computation time that is proportional to products of lengths of the strings. For example, the alignment may be determined using space that is proportional to a sum of the lengths of the data strings.
摘要翻译：提供了方法，软件安排和系统，其可以利用程序的示例性实施方案，其可以使得能够使用紧密接近一般和生物学有意义的间隙功能的分段线性间隙罚分来有效地对齐DNA序列。因此，可以提供示例性的过程，软件配置和系统来获得与在数据串中具有多个位置的至少两个数据串之间的对准相关联的数据。例如，可以使用特定功能在数据串之间提供对准的至少一个特性。该特定功能能够基于非仿射间隙罚函数来评估对准中的串之间的间隙。根据本发明的另一示例性实施例，提供了用于获得与在数据串中具有多个位置的至少两个数据串之间的对准相关联的数据的过程，软件安排和系统。具体而言，可以在与弦的长度的乘积成比例的计算时间确定在基本上所有情况下近似最佳的对准。例如，可以使用与数据串的长度的和成比例的空间来确定对准。

7. 发明授权

US08140269B2 Methods, computer-accessible medium, and systems for generating a genome wide haplotype sequence 有权
标题翻译：方法，计算机可访问介质和用于产生基因组宽单倍型序列的系统
公开(公告)号：US08140269B2
公开(公告)日：2012-03-20
申请号：US12046988
申请日：2008-03-12
申请人： Bhubaneswar Mishra , Thomas Anantharaman , Sang Lim
发明人： Bhubaneswar Mishra , Thomas Anantharaman , Sang Lim
IPC分类号： G01N33/48 , C12Q1/68 , G06G7/58
CPC分类号： G06F19/18 , G06F19/24
摘要： Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the at least one genome wide restriction map and locations of detectable oligonucleotide probes of the at least one genome wide probe map and defining a consensus map indicating restriction sites based on each of the at least one genome wide restriction map and locations of detectable oligonucleotide probes based on each of the at least one genome wide probe map.
摘要翻译：提供了用于产生基因组宽探针图和/或基因组宽单倍型序列的方法，计算机可访问介质和系统。特别地，通过获得与至少一个用至少一个限制酶切割的至少一个双链核酸分子杂交的多个可检测的寡核苷酸探针，并检测可检测的寡核苷酸探针的位置，可以产生基因组宽探针图。例如，可以通过分析至少一个基因组宽限制性图谱与至少一个基因组宽的探针图来分析至少一个全基因组限制性图谱的限制性位点与可检测的寡核苷酸探针的位置之间的距离来产生全基因组单倍型序列的所述至少一个基因组宽探针图并且基于所述至少一个全基因组限制图中的每一个和基于所述至少一个全基因组宽度探针图中的每一个的可检测寡核苷酸探针的位置来定义指示限制性位点的共有图。

8. 发明授权

US08090747B2 Method, system, computer-accessible medium and software arrangement for organization and analysis of multiple sets of data 有权
标题翻译：方法，系统，计算机可访问的介质和软件安排，用于组织和分析多组数据
公开(公告)号：US08090747B2
公开(公告)日：2012-01-03
申请号：US12124753
申请日：2008-05-21
申请人： Samantha Kleinberg , Bhubaneswar Mishra
发明人： Samantha Kleinberg , Bhubaneswar Mishra
IPC分类号： G06F17/30
CPC分类号： G06F19/24 , G06F19/22 , G06F19/26 , Y10S707/941 , Y10S707/944 , Y10S707/95
摘要： Exemplary embodiments of system, computer-accessible medium and method can be provided for organizing or analyzing at least two sets of data. The sets of data can be organized and/or analyzed by generating a data structure for the sets of data and comparing the data structure for the at least two sets of data. The data structure can be in the form of a phylogenetic-type tree, and at least one of the sets of the data can include time series data.
摘要翻译：可以提供系统，计算机可访问介质和方法的示例性实施例，用于组织或分析至少两组数据。可以通过为数据集合生成数据结构并比较至少两组数据的数据结构来组织和/或分析数据集。数据结构可以是系统发生型树的形式，并且数据集合中的至少一个可以包括时间序列数据。

9. 发明授权

US08050872B2 System and method for rapid searching of highly similar protein-coding sequences using bipartite graph matching 有权
标题翻译：使用二分图匹配快速搜索高度相似的蛋白质编码序列的系统和方法
公开(公告)号：US08050872B2
公开(公告)日：2011-11-01
申请号：US12115187
申请日：2008-05-05
申请人： Bing Sun , Jacob T. Schwartz , Ofer H. Gill , Bhubaneswar Mishra
发明人： Bing Sun , Jacob T. Schwartz , Ofer H. Gill , Bhubaneswar Mishra
IPC分类号： G06F15/00 , G06F19/00 , G11C17/00
CPC分类号： G06F19/24 , G06F19/22
摘要： An exemplary embodiment of system, computer-accessible medium and method for comparing a first genome to a second genome. For example, a first genome may be compared to a second genome by building a first library for the first genome and a second library for the second genome, providing a plurality of matches between elements in the first library common to elements in the second library, ranking each match to determine a likelihood of similarity between the common elements in the first and second libraries; and associating matches having a predetermined likelihood. The association may be performed efficiently by a stable marriage procedure.
摘要翻译：用于比较第一基因组与第二基因组的系统，计算机可访问介质和方法的示例性实施方案。例如，通过构建第一基因组的第一文库和第二基因组的第二文库，可以将第一基因组与第二基因组进行比较，提供第二文库中元素共有的第一文库中的元素之间的多个匹配，对每个匹配进行排序，以确定第一和第二文库中的共同元素之间的相似性的可能性; 以及将具有预定可能性的匹配相关联。协会可以通过稳定的婚姻程序有效地执行。

10. 发明申请

US20100293124A1 Method and System for Data Classification in the Presence of a Temporal Non-Stationarity 有权
标题翻译：时间非平稳性存在的数据分类方法与系统
公开(公告)号：US20100293124A1
公开(公告)日：2010-11-18
申请号：US12843696
申请日：2010-07-26
申请人： Gideon Berger , Bhubaneswar Mishra
发明人： Gideon Berger , Bhubaneswar Mishra
IPC分类号： G06F15/18
CPC分类号： G06K9/6217 , G06F19/20 , G06F19/24 , G06F21/552 , G06N7/005 , Y10S707/99931 , Y10S707/99932 , Y10S707/99936
摘要： A method and system for determining a feature of a particular pattern are provided. In particular, data records are received, and predetermined patterns that are associated with at least some of the data records are obtained. Using the system and method, particular information is extracted from at least a subset of the received data records, the particular information being indicative of the particular pattern in at least some of the data records. Then, it is determined whether the particular pattern is an unexpected pattern based on the obtained predetermined patterns. In addition, it is possible to classify and reduce data and/or parameters provided in the data records. First, the data records are received. Then, the data records which have at least one particular pattern are classified using a Multivariate Adaptive Regression Splines technique. Thereafter, the data and/or parameters of the classified data records are shrunk using a Stein's Estimator Rule technique.
摘要翻译：提供了一种用于确定特定图案的特征的方法和系统。特别地，接收数据记录，并且获得与至少一些数据记录相关联的预定模式。使用该系统和方法，从所接收的数据记录的至少一个子集中提取特定信息，该特定信息指示至少一些数据记录中的特定模式。然后，基于获得的预定图案来确定特定图案是否是意外图案。此外，可以对数据记录中提供的数据和/或参数进行分类和减少。首先，接收数据记录。然后，使用多变量自适应回归样条技术对具有至少一个特定模式的数据记录进行分类。此后，分类数据记录的数据和/或参数使用Stein's Estimator Rule技术收缩。

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