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    PROGRAMMABLE ITERATED ELONGATION: A METHOD FOR MANUFACTURING SYNTHETIC GENES AND COMBINATORIAL DNA AND PROTEIN LIBRARIES
    42.
    发明申请
    PROGRAMMABLE ITERATED ELONGATION: A METHOD FOR MANUFACTURING SYNTHETIC GENES AND COMBINATORIAL DNA AND PROTEIN LIBRARIES 审中-公开
    可编程迭代：制备合成基因和组合DNA和蛋白质图谱的方法

    公开(公告)号：WO2007148337A3

    公开(公告)日：2009-04-30

    申请号：PCT/IL2007000747

    申请日：2007-06-19

    Applicant: YEDA RES & DEV ,  SHAPIRO EHUD Y ,  LINSHIZ GREGORY ,  BEN-YEHEZKEL TUVAL ,  KAPLAN SHAI ,  ADAR RIVKA ,  GRONAU ILAN ,  RAVID SIVAN

    Inventor： SHAPIRO EHUD Y ,  LINSHIZ GREGORY ,  BEN-YEHEZKEL TUVAL ,  KAPLAN SHAI ,  ADAR RIVKA ,  GRONAU ILAN ,  RAVID SIVAN

    IPC: C12P19/34 ,  G06F19/22

    CPC classification number: C12N15/1089 ,  C12N15/1031 ,  C12N15/66 ,  C12Q1/686 ,  C40B50/02 ,  G06F19/22

    Abstract: A method for manufacturing synthetic genes and combinatorial DNA and protein libraries, termed here Divide and Conquer-DNA synthesis (D&C-DNA synthesis) method. The method can be used in a systematic and automated way to synthesize any long DNA molecule and, more generally, any combinatorial molecular library having the mathematical property of being a regular set of strings. The D&C-DNA synthesis method is an algorithm design paradigm that works by recursively breaking down a problem into two or more sub-problems of the same type. The division of long DNA sequences is done in silico. The assembly of the sequence is done in vitro. The D&C-DNA synthesis method protocol consists of a tree, in which each node represents an intermediate sequence. The internal nodes are created in elongation reactions from their daughter nodes, and the leaves are synthesized directly. After each elongation only one DNA strand passes to the next level in the tree until receiving the final product. Optionally and preferably, error correction is performed to correct any errors which may have occurred during the synthetic process.

    Abstract translation: 用于制造合成基因和组合DNA和蛋白质文库的方法，这里称为Div和Conquer-DNA合成（D＆C-DNA合成）方法。 该方法可以以系统和自动的方式用于合成任何长的DNA分子，更一般地，任何组合分子文库具有作为一组规则的串的数学性质。 D＆C-DNA合成方法是一种算法设计范例，通过递归地将问题分解成两个或更多个相同类型的子问题。 长DNA序列的划分是在电脑中完成的。 序列的组装在体外进行。 D＆C-DNA合成方法协议由一棵树组成，其中每个节点表示中间序列。 内部节点是在其子节点的伸长反应中产生的，叶片直接合成。 在每次延伸之后，只有一条DNA链在树中传递到下一个级别，直到接收到最终产物。 可选地，优选地，执行错误校正以校正在合成过程中可能发生的任何错误。

    PROGRAMMABLE ITERATED ELONGATION: A METHOD FOR MANUFACTURING SYNTHETIC GENES AND COMBINATORIAL DNA AND PROTEIN LIBRARIES
    44.
    发明申请
    PROGRAMMABLE ITERATED ELONGATION: A METHOD FOR MANUFACTURING SYNTHETIC GENES AND COMBINATORIAL DNA AND PROTEIN LIBRARIES 审中-公开
    可编程迭代：制备合成基因和组合DNA和蛋白质图谱的方法

    公开(公告)号：WO2007148337A2

    公开(公告)日：2007-12-27

    申请号：PCT/IL2007/000747

    申请日：2007-06-19

    Applicant: YEDA RESEARCH AND DEVELOPMENT CO. LTD. ,  SHAPIRO, Ehud Y. ,  LINSHIZ, Gregory ,  BEN-YEHEZKEL, Tuval ,  KAPLAN, Shai ,  ADAR, Rivka ,  GRONAU, Ilan ,  RAVID, Sivan

    Inventor： SHAPIRO, Ehud Y. ,  LINSHIZ, Gregory ,  BEN-YEHEZKEL, Tuval ,  KAPLAN, Shai ,  ADAR, Rivka ,  GRONAU, Ilan ,  RAVID, Sivan

    IPC: G06F19/00

    CPC classification number: C12N15/1089 ,  C12N15/1031 ,  C12N15/66 ,  C12Q1/686 ,  C40B50/02 ,  G06F19/22

    Abstract: A method for manufacturing synthetic genes and combinatorial DNA and protein libraries, termed here Divide and Conquer-DNA synthesis (D&C-DNA synthesis) method. The method can be used in a systematic and automated way to synthesize any long DNA molecule and, more generally, any combinatorial molecular library having the mathematical property of being a regular set of strings. The D&C-DNA synthesis method is an algorithm design paradigm that works by recursively breaking down a problem into two or more sub-problems of the same type. The division of long DNA sequences is done in silico. The assembly of the sequence is done in vitro. The D&C-DNA synthesis method protocol consists of a tree, in which each node represents an intermediate sequence. The internal nodes are created in elongation reactions from their daughter nodes, and the leaves are synthesized directly. After each elongation only one DNA strand passes to the next level in the tree until receiving the final product. Optionally and preferably, error correction is performed to correct any errors which may have occurred during the synthetic process.

    Abstract translation: 用于制造合成基因和组合DNA和蛋白质文库的方法，这里称为Div和Conquer-DNA合成（D＆C-DNA合成）方法。 该方法可以以系统和自动的方式用于合成任何长的DNA分子，更一般地，任何组合分子文库具有作为一组规则的串的数学性质。 D＆C-DNA合成方法是一种算法设计范例，通过递归地将问题分解成两个或更多个相同类型的子问题。 长DNA序列的划分是在电脑中完成的。 序列的组装在体外进行。 D＆C-DNA合成方法协议由一棵树组成，其中每个节点表示中间序列。 内部节点是在其子节点的伸长反应中产生的，叶片直接合成。 在每次延伸之后，只有一条DNA链在树中传递到下一个级别，直到接收到最终产物。 可选地，优选地，执行错误校正以校正在合成过程中可能发生的任何错误。

    METHOD OF CONSTRUCTING AND SCREENING LIBRARIES OF PEPTIDE STRUCTURES
    45.
    发明申请
    METHOD OF CONSTRUCTING AND SCREENING LIBRARIES OF PEPTIDE STRUCTURES 审中-公开
    构建和筛选肽结构的方法

    公开(公告)号：WO2007097923A2

    公开(公告)日：2007-08-30

    申请号：PCT/US2007003393

    申请日：2007-02-07

    Applicant: PHYLOGICA LTD ,  WATT PAUL MICHAEL ,  DUNBRACK ROLAND

    Inventor： WATT PAUL MICHAEL ,  DUNBRACK ROLAND

    IPC: C40B40/10

    CPC classification number: C07K1/047 ,  C07K1/00 ,  C07K7/08 ,  C07K14/001 ,  C12N15/1037 ,  C12N15/1072 ,  C12N15/1089 ,  C12Q1/18 ,  C40B30/02 ,  C40B40/10 ,  G01N33/6824 ,  G01N33/6845 ,  G01N2500/10 ,  G06F19/18 ,  G06F19/22

    Abstract: The present invention provides the means for producing libraries of peptide structures for drug screening applications that are capable of folding or assuming their native conformations independently of artificial scaffolds or flanking sequences in the proteins from which they are derived. The libraries can be highly diverse such that they are representative of the repertoire of protein structures existing in nature. The libraries can also be non-redundant or normalized such that the bias towards specific structures existing in source data sets and/or in nature is/are removed. In a particularly preferred embodiment, the present invention provides 30,000 independent fold structures produced by this method. The present invention also provides computer -readable media and systems comprising structural data in relation to the peptide libraries, and methods for displaying and screening the libraries.

    Abstract translation: 本发明提供用于生产用于药物筛选应用的肽结构库的方法，其能够独立于衍生自其的蛋白质中的人造支架或侧翼序列折叠或假定其天然构象。 图书馆可以是高度多样化的，因为它们代表了自然界中存在的蛋白质结构的所有组成部分。 这些库也可以是非冗余的或归一化的，使得存在于源数据集中和/或本质上的特定结构的偏移被删除。 在特别优选的实施方案中，本发明提供了通过该方法制备的30,000个独立折叠结构。 本发明还提供了包括与肽库相关的结构数据的计算机可读介质和系统，以及用于显示和筛选文库的方法。

    INFERRING FUNCTION FROM SHOTGUN SEQUENCING DATA
    47.
    发明申请
    INFERRING FUNCTION FROM SHOTGUN SEQUENCING DATA 审中-公开
    来自SHOTGUN序列数据的感染函数

    公开(公告)号：WO2005121946A3

    公开(公告)日：2007-01-25

    申请号：PCT/US2005019241

    申请日：2005-06-01

    Applicant: NEW ENGLAND BIOLABS INC ,  ROBERTS RICHARD J

    Inventor： ROBERTS RICHARD J

    IPC: C12Q1/68 ,  C12N15/10 ,  G06F9/00 ,  G06F19/00

    CPC classification number: C12N15/1034 ,  C12N15/1089

    Abstract: Methods are described for detecting genes that encode toxic proteins using maps derived from shotgun libraries by determining the presence of gaps in clone start sites on either side of open reading frames. The method is exemplified by identifying a previously unknown restriction endonuclease gene.

    Abstract translation: 描述了用于通过确定在开放阅读框的任一侧上的克隆起始位点中存在间隙来检测编码毒性蛋白的基因的方法，所述基因来自霰弹枪库。 该方法通过鉴定先前未知的限制性内切核酸酶基因来举例说明。

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