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    SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS
    1.
    发明申请
    SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS 有权

    公开(公告)号：US20210210164A1

    公开(公告)日：2021-07-08

    申请号：US17136800

    申请日：2020-12-29

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Zheng ZHANG ,  Fiona HYLAND ,  Sowmi UTIRAMERUR

    IPC: G16B30/00

    Abstract: 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.

    SYSTEMS AND METHODS FOR IDENTIFYING SEQUENCE VARIATION
    3.
    发明申请
    SYSTEMS AND METHODS FOR IDENTIFYING SEQUENCE VARIATION 审中-公开
    用于识别序列变异的系统和方法

    公开(公告)号：US20130345066A1

    公开(公告)日：2013-12-26

    申请号：US13890923

    申请日：2013-05-09

    Applicant: Life Technologies Corporation

    Inventor： Dumitru BRINZA ,  Zheng ZHANG ,  Fiona HYLAND ,  Rajesh GOTTIMUKKALA

    IPC: C12Q1/68 ,  G06F19/12

    CPC classification number: C12Q1/6874 ,  G16B5/00 ,  G16B30/00

    Abstract: Systems and method for determining variants can receive mapped reads, align flow space information to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be evaluated in a context specific manner. A list of probable variants can be provided.

    Abstract translation: 用于确定变体的系统和方法可以接收映射读取，将流空间信息对准参考的对应部分的流空间表示。 可以以上下文特定的方式评估跨越具有潜在变体的位置的读数。 可以提供可能的变体列表。

    Methods and Systems for Local Sequence Alignment
    5.
    发明申请
    Methods and Systems for Local Sequence Alignment 审中-公开
    用于局部序列比对的方法和系统

    公开(公告)号：US20140274733A1

    公开(公告)日：2014-09-18

    申请号：US14205492

    申请日：2014-03-12

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Christian Koller ,  Zheng ZHANG

    IPC: C12Q1/68

    CPC classification number: C12Q1/6874 ,  G16B30/00

    Abstract: A method for nucleic acid sequencing includes: (a) disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith; (b) exposing the template polynucleotide strands with the sequencing primer and a polymerase operably bound therewith to a series of flows of nucleotide species flowed according to a predetermined ordering; (c) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands; and (d) aligning the plurality of sequencing reads using an alignment process comprising a first set of alignment criteria or penalties that are based on biological changes in sequence and a second set of alignment criteria or penalties that are based on a sequencing error mode.

    Abstract translation: 用于核酸测序的方法包括：（a）将多个模板多核苷酸链设置在设置在传感器阵列上的多个限定的空间中，至少一些模板多核苷酸链具有测序引物和与之可操作地结合的聚合酶; （b）用测序引物和可操作地与其结合的聚合酶将模板多核苷酸链暴露于根据预定顺序流过的一系列核苷酸物质流; （c）基于核苷酸物种的流量确定多个定义空间中的模板多核苷酸链的序列信息，以产生对应于模板多核苷酸链的多个测序读数; 并且（d）使用包括基于顺序的生物变化的第一组对准标准或惩罚的对准过程对齐多个测序读数，以及基于排序误差模式的第二组比对标准或惩罚。

    SYSTEMS AND METHODS FOR ANALYZING NUCLEIC ACID SEQUENCES
    7.
    发明申请
    SYSTEMS AND METHODS FOR ANALYZING NUCLEIC ACID SEQUENCES 审中-公开

    公开(公告)号：US20200051663A1

    公开(公告)日：2020-02-13

    申请号：US16279315

    申请日：2019-02-19

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Zheng ZHANG ,  Danwei GUO ,  Yuandan LOU ,  Asim SIDDIQUI ,  Dumitru BRINZA

    IPC: G16B30/00

    Abstract: Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j)=M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read.

    SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS
    8.
    发明申请
    SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS 审中-公开

    公开(公告)号：US20180089366A1

    公开(公告)日：2018-03-29

    申请号：US15679261

    申请日：2017-08-17

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Zheng ZHANG ,  Fiona HYLAND ,  Sowmi UTIRAMERUR

    IPC: G06F19/22

    CPC classification number: G16B30/00

    Abstract: 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.

    Systems and Methods for Sequence Data Alignment Quality Assessment
    10.
    发明申请
    Systems and Methods for Sequence Data Alignment Quality Assessment 审中-公开
    序列数据对齐质量评估的系统和方法

    公开(公告)号：US20160140291A1

    公开(公告)日：2016-05-19

    申请号：US15001389

    申请日：2016-01-20

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Zheng ZHANG ,  Sowmi UTIRAMERUR ,  Fiona HYLAND

    IPC: G06F19/24 ,  G06N7/00 ,  G06N3/12 ,  G06F19/22

    CPC classification number: G16B40/00 ,  G06N3/126 ,  G06N7/005 ,  G16B30/00

    Abstract: 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.

    Abstract translation: 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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