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    Systems and methods for biopolymer engineering
    2.
    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：US08005620B2

    公开(公告)日：2011-08-23

    申请号：US10566953

    申请日：2004-07-30

    申请人： Claes Gustafsson ,  Sridhar Govindarajan ,  Jeremy Stephen Minshull

    发明人： Claes Gustafsson ,  Sridhar Govindarajan ,  Jeremy Stephen Minshull

    IPC分类号： G01N33/48 ,  G06G7/58 ,  G06F7/60 ,  G06F17/00

    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。

    DESIGN OF SYNTHETIC NUCLEIC ACIDS FOR EXPRESSION OF ENCODED PROTEINS
    6.
    发明申请
    DESIGN OF SYNTHETIC NUCLEIC ACIDS FOR EXPRESSION OF ENCODED PROTEINS 有权
    用于表达编码蛋白的合成核酸的设计

    公开(公告)号：US20100029493A1

    公开(公告)日：2010-02-04

    申请号：US12184230

    申请日：2008-07-31

    申请人： Mark Welch ,  Claes Gustafsson

    发明人： Mark Welch ,  Claes Gustafsson

    IPC分类号： C40B30/02 ,  C40B60/12

    CPC分类号： G06F19/24 ,  G06F19/20

    摘要： A method of determining a property that affects expression of polynucleotides in an expression system. A plurality of polynucleotides, each encoding a polypeptide sequence, is constructed. An amino acid is encoded a plurality of times in both a first and second polynucleotide in the plurality. The amino acid is encodable by a plurality of synonymous codons including a first codon. The first codon is in the first polynucleotide at a first frequency relative to other synonymous codons, and is in the second polynucleotide at a second frequency relative to other synonymous codons. The first and second frequencies are different. Each polynucleotide is individually expressed in the expression system to measure an expression property value of the polynucleotides, thereby determining a property that affects expression of polynucleotides. The property is an effect that a frequency of use of one or more codons has on expression of polynucleotides in the expression system.

    摘要翻译： 确定影响表达系统中多核苷酸表达的性质的方法。 构建多个编码多肽序列的多核苷酸。 氨基酸在多个第一和第二多核苷酸两者中编码多次。 氨基酸可由包括第一密码子的多个同义密码子编码。 相对于其他同义密码子，第一个密码子以第一个频率位于第一个多核苷酸中，并且相对于其他同义密码子在第二个频率处于第二个多核苷酸。 第一和第二频率是不同的。 每个多核苷酸在表达系统中单独表达以测量多核苷酸的表达特性值，从而确定影响多核苷酸表达的性质。 该性质是一种或多种密码子的使用频率对表达系统中多核苷酸表达的影响。

    Optimization of crossover points for directed evolution
    7.
    发明授权
    Optimization of crossover points for directed evolution 有权
    用于定向演化的交叉点优化

    公开(公告)号：US07620500B2

    公开(公告)日：2009-11-17

    申请号：US10386903

    申请日：2003-03-10

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

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

    IPC分类号： G01N33/48 ,  G06G7/48

    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。

    Synthetic nucleic acids for expression of encoded proteins
    8.
    发明授权
    Synthetic nucleic acids for expression of encoded proteins 有权
    用于表达编码蛋白质的合成核酸

    公开(公告)号：US07561972B1

    公开(公告)日：2009-07-14

    申请号：US12184234

    申请日：2008-07-31

    申请人： Mark Welch ,  Claes Gustafsson

    发明人： Mark Welch ,  Claes Gustafsson

    IPC分类号： G01N33/48 ,  C12Q1/00 ,  C12Q1/48 ,  C07H21/02

    CPC分类号： C12N15/67 ,  G06F19/20 ,  G06F19/22

    摘要： 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. The polynucleotide sequence is then outputted.

    摘要翻译： 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。 然后输出多核苷酸序列。

    Optimization of crossover points for directed evolution
    10.
    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。