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1. 发明申请

US20110270532A1 Systems And Methods For Identifying Exon Junctions From Single Reads 审中-公开
标题翻译：用于从单次读取中识别外显子结的系统和方法
公开(公告)号：US20110270532A1
公开(公告)日：2011-11-03
申请号：US13097328
申请日：2011-04-29
申请人： Paolo VATTA , Onur Sakarya , Heinz Breu , Liviu Popescu , Asim Siddiqui , Fiona Hyland
发明人： Paolo VATTA , Onur Sakarya , Heinz Breu , Liviu Popescu , Asim Siddiqui , Fiona Hyland
IPC分类号： G06F19/00 , G01N33/48
CPC分类号： G16B30/00
摘要： Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor.
摘要翻译：系统和方法用于从单次阅读誊本中鉴定出外显子连接。询问转录物样品，并使用核酸测序仪产生读序列。使用处理器获得第一外显子序列和第二外显子序列。使用处理器将第一个外显子序列映射到读取序列的前缀。第二个外显子序列使用处理器映射到读序列的后缀。与第一外显子序列的序列元素的数量重叠，读取序列的前缀，与重写序列的后缀重叠的第二外显子序列的多个序列元件的数目和一个常数的序列元素的总和是使用处理器。如果总和等于读取序列的长度，则使用处理器在读取中识别结。

2. 发明授权

US09268903B2 Systems and methods for sequence data alignment quality assessment 有权
标题翻译：序列数据对齐质量评估的系统和方法
公开(公告)号：US09268903B2
公开(公告)日：2016-02-23
申请号：US13177267
申请日：2011-07-06
申请人： Zheng Zhang , Sowmi Utiramerur , Fiona Hyland
发明人： Zheng Zhang , Sowmi Utiramerur , Fiona Hyland
IPC分类号： G06F19/22 , G06F15/00 , G06F19/24
CPC分类号： G06F19/24 , G06F19/22 , G06N3/126 , G06N7/005
摘要： A computer-implemented method for classifying alignments of paired nucleic acid sequence reads is disclosed. A plurality of paired nucleic acid sequence reads is received, wherein each read is comprised of a first tag and a second tag separated by an insert region. Potential alignments for the first and second tags of each read to a reference sequence is determined, wherein the potential alignments satisfies a minimum threshold mismatch constraint. Potential paired alignments of the first and second tags of each read are identified, wherein a distance between the first and second tags of each potential paired alignment is within an estimated insert size range. An alignment score is calculated for each potential paired alignment based on a distance between the first and second tags and a total number of mismatches for each tag.
摘要翻译：公开了用于分类配对核酸序列读数的计算机实现的方法。接收多个配对的核酸序列读取，其中每个读取包括由插入区域分隔的第一标签和第二标签。确定每个读取到参考序列的第一和第二标签的潜在对准，其中所述电位对准满足最小阈值失配约束。识别每个读取的第一和第二标签的潜在配对比对，其中每个潜在配对对准的第一和第二标签之间的距离在估计的插入尺寸范围内。基于第一和第二标签之间的距离和每个标签的总失配数，针对每个潜在配对对齐计算对准分数。

3. 发明申请

US20130073214A1 SYSTEMS AND METHODS FOR IDENTIFYING SEQUENCE VARIATION 审中-公开
标题翻译：用于识别序列变异的系统和方法
公开(公告)号：US20130073214A1
公开(公告)日：2013-03-21
申请号：US13623709
申请日：2012-09-20
申请人： Fiona HYLAND , Eric TSUNG , Vasisht TADIGOTLA , Zheng ZHANG , Dumitru BRINZA , Onur SAKARYA , Xing XU
发明人： Fiona HYLAND , Eric TSUNG , Vasisht TADIGOTLA , Zheng ZHANG , Dumitru BRINZA , Onur SAKARYA , Xing XU
IPC分类号： G06F19/10
CPC分类号： G16B30/00
摘要： Systems and method for determining variants can receive mapped reads, and call variants. In embodiments, flow space information for the reads can be aligned to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be grouped and a score can be calculated for the variant. Based on the scores, a list of probable variants can be provided. In various embodiments, low frequency variants can be identified where multiple potential variants are present at a position.
摘要翻译：用于确定变体的系统和方法可以接收映射读取和调用变量。在实施例中，用于读取的流动空间信息可以与参考的对应部分的流动空间表示对齐。可以将具有潜在变体的位置的读数分组，并且可以为该变体计算得分。根据分数，可以提供可能的变体列表。在各种实施例中，可以识别在一个位置存在多个潜在变体的低频变体。

4. 发明申请

US20120046877A1 SYSTEMS AND METHODS TO DETECT COPY NUMBER VARIATION 审中-公开
标题翻译：检测复制数变化的系统和方法
公开(公告)号：US20120046877A1
公开(公告)日：2012-02-23
申请号：US13176471
申请日：2011-07-05
申请人： Fiona HYLAND , Rajesh Gottimukkala
发明人： Fiona HYLAND , Rajesh Gottimukkala
IPC分类号： G06F19/00
CPC分类号： G16B30/00 , C12Q1/6809 , G16B20/00 , C12Q2535/122 , C12Q2537/16 , C12Q2537/165
摘要： In one aspect, a system for implementing a copy number variation analysis method, is disclosed. The system can include a nucleic acid sequencer and a computing device in communications with the nucleic acid sequencer. The nucleic acid sequencer can be configured to interrogate a sample to produce a nucleic acid sequence data file containing a plurality of nucleic acid sequence reads. In various embodiments, the computing device can be a workstation, mainframe computer, personal computer, mobile device, etc.The computing device can comprise a sequencing mapping engine, a coverage normalization engine, a segmentation engine and a copy number variation identification engine. The sequence mapping engine can be configured to align the plurality of nucleic acid sequence reads to a reference sequence, wherein the aligned nucleic acid sequence reads merge to form a plurality of chromosomal regions. The coverage normalization engine can be configured to divide each chromosomal region into one or more non-overlapping window regions, determine nucleic acid sequence read coverage for each window region and normalize the nucleic acid sequence read coverage determined for each window region to correct for bias. The segmentation engine can be configured to convert the normalized nucleic acid sequence read coverage for each window region to discrete copy number states. The copy number variation identification engine can be configured to identify copy number variation in the chromosomal regions by utilizing the copy number states of each window region.
摘要翻译：一方面，公开了一种用于实现副本号变更分析方法的系统。该系统可以包括与核酸测序仪通信的核酸测序仪和计算设备。核酸测序仪可配置成询问样品以产生含有多个核酸序列读数的核酸序列数据文件。在各种实施例中，计算设备可以是工作站，大型计算机，个人计算机，移动设备等。计算设备可以包括排序映射引擎，覆盖归一化引擎，分割引擎和拷贝数变更识别引擎。序列映射引擎可以被配置为将多个核酸序列读取对准参考序列，其中对齐的核酸序列读取合并以形成多个染色体区域。覆盖归一化引擎可以被配置为将每个染色体区域划分为一个或多个非重叠窗口区域，确定每个窗口区域的核酸序列读取覆盖范围，并归一化为每个窗口区域确定的核酸序列读取覆盖率以校正偏差。分割引擎可以被配置为将每个窗口区域的标准化核酸序列读取覆盖率转换为离散拷贝数状态。拷贝数变异识别引擎可以被配置为通过利用每个窗口区域的拷贝数状态来识别染色体区域中的拷贝数变化。

5. 发明申请

US20120203792A1 SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS 审中-公开
标题翻译：用于绘制序列读数的系统和方法
公开(公告)号：US20120203792A1
公开(公告)日：2012-08-09
申请号：US13363717
申请日：2012-02-01
申请人： Zheng ZHANG , Fiona HYLAND , Sowmi UTIRAMERUR
发明人： Zheng ZHANG , Fiona HYLAND , Sowmi UTIRAMERUR
IPC分类号： G06F17/30
CPC分类号： G16B30/00
摘要： Systems, methods, and computer program products for aligning a fragment sequence to a target sequencing. The alignment is allowed at most one gap, such as an insertion or a deletion. In some embodiments, both a gapped alignment and an ungapped alignment can be produced. A selection can be made between the gapped alignment and the ungapped alignment based on a quality value for each alignment.
摘要翻译：用于将片段序列与靶序列对齐的系统，方法和计算机程序产品。允许对齐至多一个间隙，例如插入或删除。在一些实施例中，可以产生间隙对准和无间隙对准。基于每个对准的质量值，可以在间隙对准和无间隙对准之间进行选择。

6. 发明申请

US20120102054A1 Systems and Methods for Annotating Biomolecule Data 审中-公开
标题翻译：用于注释生物分子数据的系统和方法
公开(公告)号：US20120102054A1
公开(公告)日：2012-04-26
申请号：US13280990
申请日：2011-10-25
申请人： Liviu POPESCU , Fiona Hyland
发明人： Liviu POPESCU , Fiona Hyland
IPC分类号： G06F17/30
CPC分类号： G06F16/24573 , G06F16/2455 , G06F16/248 , G16B40/00 , G16B50/00
摘要： Systems, methods, software and computer-usable media for annotating biomolecule-related data are disclosed. In certain exemplified embodiments, the biomolecules can be nucleic acids and the data can be sequence-related data. In various embodiments, systems can include one or more public or private biological attributes (e.g., annotation information databases, data storage devices and systems, etc.) sources, one or more genomic features data sources (e.g., genomic variant tools, genomic variant databases, genomic variant data storage devices and systems, etc.), a computing device (e.g., workstation, server, personal computer, mobile device, etc.) hosting an annotations module and/or a reporting module, and a client terminal.
摘要翻译：公开了用于注释生物分子相关数据的系统，方法，软件和计算机可用介质。在某些示例性实施方案中，生物分子可以是核酸，并且数据可以是序列相关数据。在各种实施例中，系统可以包括一个或多个公共或私人生物属性（例如，注释信息数据库，数据存储设备和系统等）源，一个或多个基因组特征数据源（例如，基因组变体工具，基因组变体数据库，基因组变体数据存储设备和系统等），托管注释模块和/或报告模块的计算设备（例如，工作站，服务器，个人计算机，移动设备等）和客户终端。

7. 发明申请

US20120011086A1 SYSTEMS AND METHODS FOR SEQUENCE DATA ALIGNMENT QUALITY ASSESSMENT 有权
标题翻译：序列数据对齐质量评估的系统和方法
公开(公告)号：US20120011086A1
公开(公告)日：2012-01-12
申请号：US13177267
申请日：2011-07-06
申请人： Zheng ZHANG , Sowmi Utiramerur , Fiona Hyland
发明人： Zheng ZHANG , Sowmi Utiramerur , Fiona Hyland
IPC分类号： G06N3/02
CPC分类号： G06F19/24 , G06F19/22 , G06N3/126 , G06N7/005
摘要： A computer-implemented method for classifying alignments of paired nucleic acid sequence reads is disclosed. A plurality of paired nucleic acid sequence reads is received, wherein each read is comprised of a first tag and a second tag separated by an insert region. Potential alignments for the first and second tags of each read to a reference sequence is determined, wherein the potential alignments satisfies a minimum threshold mismatch constraint. Potential paired alignments of the first and second tags of each read are identified, wherein a distance between the first and second tags of each potential paired alignment is within an estimated insert size range. An alignment score is calculated for each potential paired alignment based on a distance between the first and second tags and a total number of mismatches for each tag.
摘要翻译：公开了用于分类配对核酸序列读数的计算机实现的方法。接收多个配对的核酸序列读取，其中每个读取包括由插入区域分隔的第一标签和第二标签。确定每个读取到参考序列的第一和第二标签的潜在对准，其中所述电位对准满足最小阈值失配约束。识别每个读取的第一和第二标签的潜在配对比对，其中每个潜在配对对准的第一和第二标签之间的距离在估计的插入尺寸范围内。基于第一和第二标签之间的距离和每个标签的总失配数，针对每个潜在配对对齐计算对准分数。

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