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    SYSTEMS AND METHODS FOR DESIGNING AND ORDERING POLYNUCLEOTIDES
    2.
    发明申请
    SYSTEMS AND METHODS FOR DESIGNING AND ORDERING POLYNUCLEOTIDES 审中-公开
    用于设计和订购多核苷酸的系统和方法

    公开(公告)号：WO2007022260A2

    公开(公告)日：2007-02-22

    申请号：PCT/US2006/031976

    申请日：2006-08-15

    Applicant: DNA 2.0 INC. ,  GUSTAFSSON, Claes ,  GOVINDARAJAN, Sridhar ,  NESS, Jon, E. ,  VILLALOBOS, Alan, Marco ,  MINSHULL, Jeremy

    Inventor： GUSTAFSSON, Claes ,  GOVINDARAJAN, Sridhar ,  NESS, Jon, E. ,  VILLALOBOS, Alan, Marco ,  MINSHULL, Jeremy

    IPC: G06F19/00

    CPC classification number: G06F19/26 ,  G06F19/18 ,  G06F19/20

    Abstract: Computer systems, computer program products and methods for designing oligonucleotides are provided. A set of sequence elements is defined. Each sequence element represents an amino acid sequence segment or a nucleic acid sequence segment. The set of sequence elements collectively represent a design nucleic acid sequence. The set of sequence elements are displayed as a plurality of icons in a linear or a near linear arrangement such that each respective icon in the plurality of icons uniquely represents a corresponding sequence element in the set of sequence elements. In this representation, neighboring icons in the plurality of icons represent neighboring sequence elements in the set of sequence elements. Each respective icon in the plurality of icons depicts a directional property for the corresponding sequence element in the set of sequence elements. An oligonucleotide selection module is used to identify oligonucleotides in the design nucleic acid sequence.

    Abstract translation: 提供了用于设计寡核苷酸的计算机系统，计算机程序产品和方法。 定义了一组序列元素。 每个序列元件代表氨基酸序列区段或核酸序列区段。 该组序列元件共同表示设计核酸序列。 该组序列元素以线性或近似线性排列显示为多个图标，使得多个图标中的每个相应图标唯一地表示该组序列元素中的对应序列元素。 在该表示中，多个图标中的相邻图标表示该组序列元素中的相邻序列元素。 多个图标中的每个相应图标描绘了该组序列元素中的对应序列元素的方向属性。 寡核苷酸选择模块用于鉴定设计核酸序列中的寡核苷酸。

    SYSTEMS AND METHODS FOR ANTIBODY ENGINEERING
    3.
    发明申请
    SYSTEMS AND METHODS FOR ANTIBODY ENGINEERING 审中-公开
    用于抗体工程的系统和方法

    公开(公告)号：WO2005012877A3

    公开(公告)日：2006-04-06

    申请号：PCT/US2004024751

    申请日：2004-07-30

    Applicant: DNA TWOPOINTO INC ,  GUSTAFSSON CLAES ,  GOVINDARAJAN SRIDHAR ,  MINSHULL JEREMY STEPHEN

    Inventor： GUSTAFSSON CLAES ,  GOVINDARAJAN SRIDHAR ,  MINSHULL JEREMY STEPHEN

    IPC: C07K16/10 ,  C07K16/46 ,  G01N20060101 ,  G06F20060101 ,  G06F19/16 ,  G06F19/18 ,  G06F19/24 ,  G01N33/00 ,  G01N33/48

    CPC classification number: G06F19/18 ,  C07K16/1027 ,  C07K16/461 ,  C07K2317/76 ,  G06F19/16 ,  G06F19/24

    Abstract: Methods, computer systems, and computer program products for antibody engineering. A variant set for an antibody of interest is constructed by identifying, using a plurality of roles, a plurality of positions in the antibody of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions and the substitutions for each respective position in the plurality of positions collectively define an antibody sequence space. A variant set comprising a plurality of variants of the antibody of interest is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-activity relationship is modeled between (i) one or more substitutions at one or more positions of the antibody of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set. The variant set is redefined to comprise variants that include substitutions in the plurality of positions that are selected based on a function of the sequence-activity relationship.

    Abstract translation: 方法，计算机系统和抗体工程的计算机程序产品。 通过使用多个角色来鉴定感兴趣的抗体中的多个位置，并且对于多个位置中的每个相应位置，通过识别相应位置的替换来构建用于感兴趣抗体的变体。 多个位置中的各个位置的多个位置和替换共同限定抗体序列空间。 选择包含感兴趣抗体的多个变体的变体集合。 测量变体集中全部或部分变体的属性。 在（i）由变体组表示的感兴趣抗体的一个或多个位置处的一个或多个取代和（ii）针对变体组中的全部或部分变体测量的性质之间建立序列活性关系。 变体集被重新定义为包括基于序列活动关系的函数而选择的多个位置中的替换的变体。

    METHODS, SYSTEMS, AND SOFTWARE FOR REGULATED OLIGONUCLEOTIDE-MEDIATED RECOMBINATION
    6.
    发明申请
    METHODS, SYSTEMS, AND SOFTWARE FOR REGULATED OLIGONUCLEOTIDE-MEDIATED RECOMBINATION 审中-公开
    用于调控寡核苷酸介导的重组的方法，系统和软件

    公开(公告)号：WO2008127213A2

    公开(公告)日：2008-10-23

    申请号：PCT/US2002/014866

    申请日：2002-05-09

    Applicant: MAXYGEN, INC. ,  MINSHULL, Jeremy ,  GUSTAFSSON, Claes ,  GOVINDARAJAN, Sridar ,  ROY, Ajoy

    Inventor： MINSHULL, Jeremy ,  GUSTAFSSON, Claes ,  GOVINDARAJAN, Sridar ,  ROY, Ajoy

    IPC: C12Q1/68

    CPC classification number: G06F19/22 ,  B01J2219/007 ,  B01J2219/00722 ,  C12N15/1089 ,  C12Q1/6806 ,  C12Q2531/113

    Abstract: The present invention provides novel in silico recombination techniques in which all or part of a nucleic acid recombination procedure is performed or modeled in a digital system. In particular, this invention relates to methods of designing oligonucleotides for regulated recombination that approximates linkage characteristics obtained from fragmentation-based recombination techniques, such as family-based recombination. The methods of this invention include adjusting overlap regions in pairs of overlapping oligonucleotide character strings to bias recombination towards a desired genetic linkage. This invention also provides systems, computer program products, and kits for practicing the methods of the invention.

    Abstract translation: 本发明提供新颖的计算机重组技术，其中全部或部分核酸重组程序在数字系统中进行或模拟。 具体而言，本发明涉及设计用于调控重组的寡核苷酸的方法，其接近从基于片段化的重组技术获得的连锁特征，例如基于家族的重组。 本发明的方法包括调整重叠的寡核苷酸字符串对中的重叠区域以偏向重要的遗传连锁。 本发明还提供用于实施本发明方法的系统，计算机程序产品和试剂盒。

    SYSTEMS AND METHODS FOR ANTIBODY ENGINEERING
    7.
    发明申请
    SYSTEMS AND METHODS FOR ANTIBODY ENGINEERING 审中-公开
    用于抗体工程的系统和方法

    公开(公告)号：WO2005012877A2

    公开(公告)日：2005-02-10

    申请号：PCT/US2004/024751

    申请日：2004-07-30

    Applicant: DNA TWOPOINTO INC. ,  GUSTAFSSON, Claes ,  GOVINDARAJAN, Sridhar ,  MINSHULL, Jeremy, Stephen

    Inventor： GUSTAFSSON, Claes ,  GOVINDARAJAN, Sridhar ,  MINSHULL, Jeremy, Stephen

    IPC: G01N

    CPC classification number: G06F19/18 ,  C07K16/1027 ,  C07K16/461 ,  C07K2317/76 ,  G06F19/16 ,  G06F19/24

    Abstract: Methods, computer systems, and computer program products for antibody engineering. A variant set for an antibody of interest is constructed by identifying, using a plurality of roles, a plurality of positions in the antibody of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions and the substitutions for each respective position in the plurality of positions collectively define an antibody sequence space. A variant set comprising a plurality of variants of the antibody of interest is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-activity relationship is modeled between (i) one or more substitutions at one or more positions of the antibody of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set. The variant set is redefined to comprise variants that include substitutions in the plurality of positions that are selected based on a function of the sequence-activity relationship.

    Abstract translation: 方法，计算机系统和抗体工程的计算机程序产品。 通过使用多个角色来识别感兴趣抗体中的多个位置，并且对于多个位置中的每个相应位置，通过识别相应位置的替换来构建用于感兴趣抗体的变体。 多个位置中的各个位置的多个位置和替换共同限定抗体序列空间。 选择包含感兴趣的抗体的多个变体的变体组。 测量变体集中全部或部分变体的属性。 在（i）由变体组表示的感兴趣抗体的一个或多个位置处的一个或多个取代和（ii）针对变体组中全部或部分变体测量的性质的序列活性关系进行建模。 变体集被重新定义为包括在基于序列活动关系的函数选择的多个位置中的替换的变体。

    SYSTEMS AND METHODS FOR DETERMINING PROPERTIES THAT AFFECT AN EXPRESSION PROPERTY VALUE OF POLYNUCLEOTIDES IN AN EXPRESSION SYSTEM
    10.
    发明申请
    SYSTEMS AND METHODS FOR DETERMINING PROPERTIES THAT AFFECT AN EXPRESSION PROPERTY VALUE OF POLYNUCLEOTIDES IN AN EXPRESSION SYSTEM 审中-公开
    用于确定在表达系统中影响多核苷酸的表达性质的性质的系统和方法

    公开(公告)号：WO2009148616A2

    公开(公告)日：2009-12-10

    申请号：PCT/US2009/003412

    申请日：2009-06-05

    Applicant: DNA 2.0 INC. ,  WELCH, Mark ,  GUSTAFSSON, Claes

    Inventor： WELCH, Mark ,  GUSTAFSSON, Claes

    IPC: C40B30/02 ,  C40B60/12

    CPC classification number: C12N15/67 ,  G06F19/20 ,  G06F19/22

    Abstract: A method of designing a polynucleotide sequence encoding a polypeptide sequence of a predetermined polypeptide is provided. A frequency lookup table corresponding to an expression system is obtained. The table comprises a plurality of sequence elements and a plurality of frequency ranges, each frequency range for a corresponding sequence element. Each frequency range is a range of frequencies with which a corresponding sequence element can occur in a polynucleotide. The polynucleotide sequence is defined using the frequency lookup table by determining, for each respective sequence element in the frequency lookup table, whether the respective sequence element encodes a portion of the polypeptide sequence. When the respective sequence element encodes a portion of the polypeptide sequence, the sequence element is incorporated into the polynucleotide at a frequency of occurrence that is within the frequency range specified for the respective sequence element in the lookup table.

    Abstract translation: 提供了设计编码预定多肽的多肽序列的多核苷酸序列的方法。 获得与表达式系统对应的频率查找表。 该表包括多个序列元素和多个频率范围，每个频率范围用于相应的序列元素。 每个频率范围是在多核苷酸中可以发生相应序列元件的频率范围。 使用频率查找表来定义多核苷酸序列，对于频率查找表中的每个相应序列元件，确定各个序列元件是否编码多肽序列的一部分。 当各个序列元件编码多肽序列的一部分时，序列元件以在查找表中对于相应序列元件指定的频率范围内的发生频率被并入多核苷酸。

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