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    • 4. 发明申请
    • SYSTEMS AND METHODS FOR DESIGNING AND ORDERING POLYNUCLEOTIDES
    • 用于设计和订购多核苷酸的系统和方法
    • WO2007022260A3
    • 2008-08-28
    • PCT/US2006031976
    • 2006-08-15
    • DNA 2 0 INCGUSTAFSSON CLAESGOVINDARAJAN SRIDHARNESS JON EVILLALOBOS ALAN MARCOMINSHULL JEREMY
    • GUSTAFSSON CLAESGOVINDARAJAN SRIDHARNESS JON EVILLALOBOS ALAN MARCOMINSHULL JEREMY
    • G06F7/00
    • G06F19/26G06F19/18G06F19/20
    • 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.
    • 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图标描绘了该组序列元素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。
    • 5. 发明申请
    • SYSTEMS AND METHODS FOR BIOPOLYMER ENGINEERING
    • 生物聚合物工程系统与方法
    • WO2005013090A3
    • 2006-04-13
    • PCT/US2004024752
    • 2004-07-30
    • DNA TWOPOINTO INCGUSTAFSSON CLAESGOVINDARAJAN SRIDHARMINSHULL JEREMY STEPHEN
    • GUSTAFSSON CLAESGOVINDARAJAN SRIDHARMINSHULL JEREMY STEPHEN
    • C07K16/10C07K16/46G01N20060101G06F20060101G06F19/16G06F19/18G06F19/24G01N33/00G01N33/48
    • G06F19/18C07K16/1027C07K16/461C07K2317/76G06F19/16G06F19/24
    • 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.
    • 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换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。 序列活性关系在(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)针对变体集中的全部或部分变体测量的性质之间建模。 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。