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1. 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。

2. 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。

3. 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。

4. 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。

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