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1. 发明申请

US20120330563A1 Assembly Error Detection 审中-公开
标题翻译：装配错误检测
公开(公告)号：US20120330563A1
公开(公告)日：2012-12-27
申请号：US13605119
申请日：2012-09-06
申请人： Laxmi P. Parida , Niina Haiminen
发明人： Laxmi P. Parida , Niina Haiminen
IPC分类号： G06F19/24
CPC分类号： G16B99/00
摘要： A method for detecting errors in genetic sequence assemblies including defining an assembly (A) of a sequence of genetic data, collecting read data into a library of reads (L), plotting histograms of sizes or reads versus a number of reads per size, normalizing a distribution (D) with a coverage C to obtain D′ that has a mean (μ) and standard deviation (σ) and reserve positions (i) not used to obtain D′, collecting subset of reads (Si⊂L) using A and D′, computing mean (μi) and standard deviation (√ci·σi) using Si, outputting results to user on a display.
摘要翻译：一种用于检测遗传序列组合中的错误的方法，包括定义遗传数据序列的组件（A），将读取的数据收集到读取库（L）中，绘制大小或读取的直方图与每个大小的读数，归一化具有覆盖度C的分布（D）以获得具有平均值（μ）和标准偏差（＆sgr）的D'和未用于获得D'的储备位置（i），收集读取子集（Si⊂L） A和D'，使用Si计算平均值（μi）和标准偏差（√ci·＆sgr; i），将结果输出到显示器上的用户。

2. 发明申请

US20100049685A1 Pattern Discovery Techniques for Determining Maximal Irredundant and Redundant Motifs 审中-公开
标题翻译：用于确定最大不饱和和冗余主题的模式发现技术
公开(公告)号：US20100049685A1
公开(公告)日：2010-02-25
申请号：US12533251
申请日：2009-07-31
申请人： Laxmi P. Parida
发明人： Laxmi P. Parida
IPC分类号： G06N5/02
CPC分类号： G01N33/6803 , G16B30/00 , G16B40/00
摘要： Basis motifs are determined from an input sequence through an iterative technique that begins by creating small solid motifs and continues to create larger motifs that include “don't care” characters and that can include flexible portions. The small solid motifs, including don't care characters and flexible portions, are concatenated to create larger motifs. During each iteration, motifs are trimmed to remove redundant motifs and other motifs that do not meet certain criteria. The process is continued until no new motifs are determined. At this point, the basis set of motifs has been determined. The basis motifs are used to construct redundant motifs. The redundant motifs are formed by determining a number of sets for selected basis motifs. From these sets, unique intersection sets are determined. The redundant motifs are determined from the unique intersection sets and the basis motifs. This process continues, by selecting additional basis motifs, until all basis motifs have been selected.
摘要翻译：基本图案通过迭代技术从输入序列确定，该技术从创建小的实体图案开始，并继续创建包括“不关心”字符并且可以包括柔性部分的较大图案。小的实心图案，包括不关心角色和柔性部分，连接起来以创建更大的图案。在每次迭代期间，修剪图案以去除不符合某些标准的冗余图案和其他图案。该过程一直持续到没有确定新的图案。在这一点上，基本的图案已经确定了。基本图案用于构建冗余图案。冗余图案通过确定所选择的基础图案的多个组来形成。从这些集合中，确定唯一的交集。冗余图案是从独特的交集和基础图案确定的。通过选择附加基本图案，继续进行所有基本图案的选择。

3. 发明申请

US20100049449A1 Pattern Discovery Techniques for Determining Maximal Irredundant and Redundant Motifs 失效
公开(公告)号：US20100049449A1
公开(公告)日：2010-02-25
申请号：US12533221
申请日：2009-07-31
申请人： Laxmi P. Parida
发明人： Laxmi P. Parida
IPC分类号： G06F19/00
CPC分类号： G06F19/24 , G01N33/6803 , G06F19/22
摘要： Basis motifs are determined from an input sequence through an iterative technique that begins by creating small solid motifs and continues to create larger motifs that include “don't care” characters and that can include flexible portions. The small solid motifs, including don't care characters and flexible portions, are concatenated to create larger motifs. During each iteration, motifs are trimmed to remove redundant motifs and other motifs that do not meet certain criteria. The process is continued until no new motifs are determined. At this point, the basis set of motifs has been determined. The basis motifs are used to construct redundant motifs. The redundant motifs are formed by determining a number of sets for selected basis motifs. From these sets, unique intersection sets are determined. The redundant motifs are determined from the unique intersection sets and the basis motifs. This process continues, by selecting additional basis motifs, until all basis motifs have been selected.

4. 发明申请

US20080250002A1 OBJECT CLASSIFICATION 有权
标题翻译：对象分类
公开(公告)号：US20080250002A1
公开(公告)日：2008-10-09
申请号：US12139894
申请日：2008-06-16
申请人： Laxmi P. Parida , Ajay K. Royyuru
发明人： Laxmi P. Parida , Ajay K. Royyuru
IPC分类号： G06F7/06 , G06F17/30
CPC分类号： G06F17/3071 , G06F17/30943 , Y10S707/99932
摘要： Classification of objects using the best boolean expression that represents the most optimal combination of the underlying features is disclosed.
摘要翻译：公开了使用表示底层特征的最佳组合的最佳布尔表达式的对象的分类。

5. 发明授权

US10468122B2 Exact haplotype reconstruction of F2 populations 有权
公开(公告)号：US10468122B2
公开(公告)日：2019-11-05
申请号：US13529476
申请日：2012-06-21
申请人： Niina S. Haiminen , Laxmi P. Parida , Filippo Utro
发明人： Niina S. Haiminen , Laxmi P. Parida , Filippo Utro
IPC分类号： G16B45/00 , G06F17/16 , G16B20/00
摘要： Various embodiments reconstruct haplotypes from genotype data. In one embodiment, a set of progeny genotype data comprising n progenies encoded with m genetic markers is accessed. A first set of parent haplotypes associated with a first parent of the n progenies and a second set of parent haplotypes associated with a second parent of the n progenies are identified based on at least the set of progeny genotype data. A total minimum number of observable crossovers in the n progenies is determined. An agglomerate data structure comprising a collection of sets of haplotype sequences characterizing the n progenies is constructed based on the set of progeny genotype data and the first and second sets of parent haplotypes. Each set of haplotype sequences includes a number of crossovers equal to the total minimum number of observable crossovers in the n progenies.

6. 发明授权

US08645074B2 Method for reconstructing evolutionary data 失效
标题翻译：重建进化数据的方法
公开(公告)号：US08645074B2
公开(公告)日：2014-02-04
申请号：US11942022
申请日：2007-11-19
申请人： Laxmi P. Parida
发明人： Laxmi P. Parida
IPC分类号： G06F19/00 , G06F19/14 , G06F19/10 , G06F17/10 , G06F7/58
CPC分类号： G06F19/14
摘要： Techniques for reconstructing evolutionary data of a set of genomic data are provided. The techniques include obtaining a set of genomic data, determining a chronological order of one or more mutations within the set of genomic data, determining a chronological order of one or more recombinations within the set of genomic data, determining a position of each recombination within the set of genomic data, and combining the chronological order of the one or more mutations, the chronological order of the one or more recombinations and the position of each recombination to reconstruct evolutionary data of the set of genomic data.
摘要翻译：提供了用于重建一组基因组数据的进化数据的技术。所述技术包括获得一组基因组数据，确定该组基因组数据内的一个或多个突变的时间顺序，确定该组基因组数据内的一个或多个重组的时间顺序，确定基因组数据内每个重组的位置一组基因组数据，并结合一个或多个突变的时间顺序，一个或多个重组的时间顺序和每个重组的位置以重建该组基因组数据的进化数据。

7. 发明申请

US20120331008A1 SAMPLING THE SPACE OF ANCESTRAL RECOMBINATION GRAPHS 失效
标题翻译：取样片段重建图谱
公开(公告)号：US20120331008A1
公开(公告)日：2012-12-27
申请号：US13169824
申请日：2011-06-27
申请人： Laxmi P. PARIDA , Asif Javed
发明人： Laxmi P. PARIDA , Asif Javed
IPC分类号： G06F17/30
CPC分类号： G06F17/30958 , G06F17/30327 , G06F17/30625 , G06F17/30961 , Y10S707/956
摘要： A method is provided for constructing an ancestral recombination graph. A value K is received representing K extant units. M non-mixing segments are also received. K vertices V are generated. K lineages for each of M trees are associated with each of the K vertices. An ancestral recombination graph is constructed. To construct the ancestral recombination graph, there is repeated, until only one lineage survives for each of the M trees, a process that includes the following. A tree is randomly selected tree. A first vertex v1 and a second vertex v2 are randomly selected. Two adjoining segments in the M non-mixing segments of the first and second vertices are combined together into a single vertex. A separate vertex is generated for at least one remaining segment in each of the M non-mixing segments of the first and second vertices. The vertices V are updated to be vertices that are non-interior vertices.
摘要翻译：提供了一种构建祖先重组图的方法。接收表示K个存在单元的值K. 还收到M个非混合段。生成K个顶点V。每个M树的K谱系与K个顶点中的每一个相关联。构建祖先重组图。为了构建祖先重组图，重复一遍，直到每个M树只有一个谱系存活，这个过程包括如下。树是随机选择的树。随机选择第一顶点v1和第二顶点v2。第一和第二顶点的M个非混合段中的两个邻接段被组合成一个顶点。为第一和第二顶点的M个非混合段中的每一个中的至少一个剩余段生成单独的顶点。顶点V被更新为非内部顶点的顶点。

8. 发明申请

US20120191356A1 Assembly Error Detection 审中-公开
标题翻译：装配错误检测
公开(公告)号：US20120191356A1
公开(公告)日：2012-07-26
申请号：US13010949
申请日：2011-01-21
申请人： Laxmi P. Parida , Niina Haiminen
发明人： Laxmi P. Parida , Niina Haiminen
IPC分类号： G06F19/00 , G06F17/18
CPC分类号： G16B99/00
摘要： A method for detecting errors in genetic sequence assemblies including defining an assembly (A) of a sequence of genetic data, collecting read data into a library of reads (L), plotting histograms of sizes or reads versus a number of reads per size, normalizing a distribution (D) with a coverage C to obtain D′ that has a mean (μ) and standard deviation (σ) and reserve positions (i) not used to obtain D′, collecting subset of reads (Si □ L) using A and D′, computing mean (μi) and standard deviation (√ci·σi) using Si, outputting results to user on a display.
摘要翻译：一种用于检测遗传序列组合中的错误的方法，包括定义遗传数据序列的组件（A），将读取的数据收集到读取库（L）中，绘制大小或读取的直方图与每个大小的读数，归一化具有覆盖C的分布（D）以获得具有平均值（μ）和标准偏差（＆sgr）的D'和未用于获得D'的预留位置（i），收集读取子集（Si□L），使用 A和D'，使用Si计算平均值（μi）和标准偏差（√ci·＆sgr; i），将结果输出到显示器上的用户。

9. 发明申请

US20090030912A1 SIGNIFICANCE MEASURE OF STRUCTURED CLUSTERS 失效
标题翻译：结构集群的意义测量
公开(公告)号：US20090030912A1
公开(公告)日：2009-01-29
申请号：US11781653
申请日：2007-07-23
申请人： Laxmi P. Parida
发明人： Laxmi P. Parida
IPC分类号： G06F17/30
CPC分类号： G06K9/62 , G06F19/24
摘要： The exemplary embodiments provide a computer implemented method, apparatus, and computer usable program code for calculating a probability. An input is received, wherein the input comprises a PQ tree. The leaf nodes of the PQ tree are counted to form a number of leaf nodes. A factorial value of the number of leaf nodes is calculated to form a denominator. A hash value of a frontier of all permutations of the PQ tree is calculated to form a numerator. A ratio of the numerator to the denominator is determined to form a result. The result is displayed to a user.
摘要翻译：示例性实施例提供用于计算概率的计算机实现的方法，装置和计算机可用程序代码。接收输入，其中输入包括PQ树。 PQ树的叶节点被计数以形成多个叶节点。计算叶节点数的阶乘值以形成分母。计算PQ树的所有排列的边界的散列值以形成分子。确定分子与分母的比例以形成结果。结果显示给用户。

10. 发明授权

US07428515B2 Object classification using an optimized Boolean expression 失效
标题翻译：使用优化布尔表达式的对象分类
公开(公告)号：US07428515B2
公开(公告)日：2008-09-23
申请号：US10676448
申请日：2003-09-30
申请人： Laxmi P. Parida , Ajay K. Royyuru
发明人： Laxmi P. Parida , Ajay K. Royyuru
IPC分类号： G06E1/00
CPC分类号： G06F17/3071 , G06F17/30943 , Y10S707/99932
摘要： Classification of objects using the best boolean expression that represents the most optimal combination of the underlying features is disclosed.
摘要翻译：公开了使用表示底层特征的最佳组合的最佳布尔表达式的对象的分类。

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