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    Systems and methods for biopolymer engineering
    37.
    发明授权
    Systems and methods for biopolymer engineering 有权
    生物聚合物工程的系统和方法

    公开(公告)号：US08635029B2

    公开(公告)日：2014-01-21

    申请号：US12238216

    申请日：2008-09-25

    申请人： Claes Gustafsson ,  Sridhar Govindarajan ,  Jeremy Minshull

    发明人： Claes Gustafsson ,  Sridhar Govindarajan ,  Jeremy Minshull

    IPC分类号： G06F7/00

    CPC分类号： G06F19/18

    摘要： Methods, computer systems, and computer program products for biopolymer engineering. A variant set for a biopolymer of interest is constructed by identifying, using a plurality of rules, a plurality of positions in the biopolymer 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 a biopolymer sequence space. A variant set comprising a plurality of variants of the biopolymer 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 biopolymer 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.

    摘要翻译： 方法，计算机系统和生物聚合物工程的计算机程序产品。 通过使用多个规则来识别感兴趣的生物聚合物中的多个位置，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代来构建用于感兴趣的生物聚合物的变体。 多个位置中的各个位置的多个位置和替换共同限定生物聚合物序列空间。 选择包含感兴趣的生物聚合物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的生物聚合物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特性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 designing and ordering polynucleotides
    38.
    发明申请
    Systems and methods for designing and ordering polynucleotides 有权
    用于设计和排序多核苷酸的系统和方法

    公开(公告)号：US20070043516A1

    公开(公告)日：2007-02-22

    申请号：US11207151

    申请日：2005-08-16

    申请人： Claes Gustafsson ,  Sridhar Govindarajan ,  Jon Ness ,  Alan Villalobos ,  Jeremy Minshull

    发明人： Claes Gustafsson ,  Sridhar Govindarajan ,  Jon Ness ,  Alan Villalobos ,  Jeremy Minshull

    IPC分类号： G06F19/00

    CPC分类号： G06F19/26 ,  G06F19/18 ,  G06F19/20

    摘要： 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 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.

    摘要翻译： 提供计算机系统，计算机程序产品和设计寡核苷酸的方法。 定义了一组序列元素。 每个序列元件代表氨基酸序列片段或核酸序列片段。 序列元件的集合统称为设计核酸序列。 序列元素的集合被显示为线性或近似线性布置的多个图标，使得多个图标中的每个相应图标唯一地表示序列元素集合中的相应序列元素。 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的图标描绘了序列元素集合中相应的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。

    Optimization of crossover points for directed evolution
    40.
    发明申请
    Optimization of crossover points for directed evolution 失效
    用于定向演化的交叉点优化

    公开(公告)号：US20080020397A1

    公开(公告)日：2008-01-24

    申请号：US11818237

    申请日：2007-06-12

    申请人： Emily Mundorff ,  Sridhar Govindarajan ,  Claes Gustafsson ,  Jeremy Minshull

    发明人： Emily Mundorff ,  Sridhar Govindarajan ,  Claes Gustafsson ,  Jeremy Minshull

    IPC分类号： C12Q1/68 ,  G01N33/53 ,  G06F19/00

    CPC分类号： G06F19/22 ,  C40B50/02 ,  G06F19/16

    摘要： Methods and devices for more efficiently engineering diversity into recombinant polypeptides and/or nucleic acids are provided herein. For example, a variety of methods of selecting and/or assessing potential crossover sites in an amino acid sequence or a nucleotide sequence are provided, as well as the resulting chimeric product sequences. These methods include, e.g., consideration of structural, functional and/or statistical data in the selection and assessment of sequences and crossover sites for use in recombination.

    摘要翻译： 本文提供了用于更有效地将多样性工程化成重组多肽和/或核酸的方法和装置。 例如，提供了选择和/或评估氨基酸序列或核苷酸序列中的潜在交叉位点的各种方法，以及所得嵌合产物序列。 这些方法包括例如考虑用于重组的序列和交换位点的选择和评估中的结构，功能和/或统计数据。