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1. 发明专利

JP2011040068A Method of populating data structure for use in evolutionary simulation 审中-公开
标题翻译：在演化模拟中使用数据结构的方法
公开(公告)号：JP2011040068A
公开(公告)日：2011-02-24
申请号：JP2010179767
申请日：2010-08-10
申请人： Maxygen Inc , マキシジェン, インコーポレイテッド
发明人： SLIFONOV SERGEY A , STEMMER WILLEM P C
IPC分类号： G06N3/00 , C12N15/09 , G06F19/00 , G06F19/14 , G06N3/12
摘要： PROBLEM TO BE SOLVED: To provide a method of populating data structures for use in evolutionary simulations. SOLUTION: There is provided novel methods of populating data structures for use in evolutionary simulations and provides methods of populating a data structure with a plurality of character strings. The methods involve: encoding two or more biological molecules into character strings to provide a collection of two or more different initial character strings; selecting at least two substrings from the pool of character strings; concatenating the substrings to form one or more product strings about the same length as one or more of the initial character strings; adding the product strings to a collection of strings; and optionally repeating this process using one or more of the product strings as an initial string in the collection of initial character strings. COPYRIGHT: (C)2011,JPO&INPIT
摘要翻译：要解决的问题：提供一种填充用于进化模拟的数据结构的方法。解决方案：提供了用于填充用于进化模拟的数据结构的新颖方法，并提供了使用多个字符串填充数据结构的方法。所述方法涉及：将两个或多个生物分子编码成字符串以提供两个或多个不同的初始字符串的集合; 从字符串池中选择至少两个子字符串; 连接子串以形成与一个或多个初始字符串相同长度的一个或多个产品串; 将产品字符串添加到字符串集合中; 并且可选地使用一个或多个产品串将该过程重复为初始字符串的集合中的初始字符串。版权所有（C）2011，JPO＆INPIT

2. 发明专利

JP2010131014A Evolution of whole cells and organisms by recursive sequence recombination 审中-公开
标题翻译：通过重新序列重组实现全细胞和有机体的发育
公开(公告)号：JP2010131014A
公开(公告)日：2010-06-17
申请号：JP2009288163
申请日：2009-12-18
申请人： Maxygen Inc , マキシジェン, インコーポレイテッド
发明人： DEL CARDAYRE STEPHEN , TOBIN MATTHEW , STEMMER WILLEM P C , NESS JON E , MINSHULL JEREMY , PATTEN PHILIP A , SUBRAMANIAN VENKITESWATAN , CASTLE LINDA A , KREBBER CLAUS M , BASS STEVE , ZHANG YING-XIN , COX TONY , HUISMAN GJALT , YUAN LING , AFFHOLTER JOSEPH A
IPC分类号： A01H1/00 , A01H5/00 , A01K67/02 , A01K67/027 , C07K14/245 , C12N1/19 , C12N5/10 , C12N15/09 , C12N15/10 , C12N15/82 , C12P17/16 , C12Q1/68
CPC分类号： C12N15/102 , C07K14/245 , C12N15/1027 , C12N15/8271 , C12N15/8273 , C12N15/8279 , C12P17/162 , C12Q1/68 , C12Q1/6811 , C12Q1/6827 , C12R1/465
摘要： PROBLEM TO BE SOLVED: To provide a novel and a large number of molecular genetic methods and compositions for evolution of whole and partial genomes. SOLUTION: The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties (including enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites). For example, methods includes the steps of fertilizing pooled male-female gametes derived from different species, growing it up to be a reproducibly survival organism, preparing an organism library of various multicellular organisms by repeating the mating process, and selecting an organism having a desired trait or property. COPYRIGHT: (C)2010,JPO&INPIT
摘要翻译：要解决的问题：提供用于全部和部分基因组进化的新颖和大量的分子遗传方法和组合物。解决方案：本发明提供了采用迭代循环重复和选择/筛选整个细胞和生物体以获得所需性质（包括增强的重组原型，基因组拷贝数以及蛋白质表达和/或分泌能力的方法）的方法，次级代谢物）。例如，方法包括以下步骤：对来自不同物种的合并雄性 - 雌性配子进行施肥，将其生长成可重复存活的生物，通过重复交配过程制备各种多细胞生物的生物文库，并选择具有所需的生物体特征或财产。版权所有（C）2010，JPO＆INPIT

3. 发明专利

JP2007244399A Dna mutagenesis by random fragmentation and reassembly 审中-公开
标题翻译： DNA随机分解和重新组装
公开(公告)号：JP2007244399A
公开(公告)日：2007-09-27
申请号：JP2007180396
申请日：2007-07-09
申请人： Maxygen Inc , マキシジェン, インコーポレイテッド
发明人： STEMMER WILLEM P C , CRAMERI ANDREAS
IPC分类号： C12N15/09 , A61K38/00 , A61K39/395 , C07K14/435 , C07K14/545 , C07K16/00 , C12N9/38 , C12N9/86 , C12N15/00 , C12N15/10 , C12P21/08 , C12Q1/68 , C40B40/02 , G01N33/53 , G01N33/566
CPC分类号： C40B40/02 , C07K14/43595 , C07K14/545 , C07K16/00 , C07K2317/565 , C07K2317/622 , C12N9/2471 , C12N9/86 , C12N15/1027 , C12N15/1034 , C12N15/1037 , C12Q1/68 , C12Q1/6811 , C12Y302/01023 , C12Y305/02006 , C40B40/08 , C40B50/06
摘要： PROBLEM TO BE SOLVED: To provide a method for generating mutant proteins and a method for developing a readily searchable large-scale library of mutant nucleic acid sequences. SOLUTION: Disclosed are a method for DNA reassembly after random fragmentation, and its application to mutagenesis of nucleic acid sequences by in vitro or in vivo recombination. In particular, a method for generating nucleic acid fragments or polynucleotides encoding the mutant proteins is disclosed. The present invention also relates to a method of repeated cycles of mutagenesis, shuffling and selection which allow for the directed molecular evolution in vitro or in vivo of proteins. COPYRIGHT: (C)2007,JPO&INPIT
摘要翻译：待解决的问题：提供产生突变蛋白的方法和开发易于搜索的突变核酸序列的大规模文库的方法。解决方案：公开了随机断裂后DNA重组的方法，以及其通过体外或体内重组诱变核酸序列的应用。特别地，公开了产生编码突变蛋白的核酸片段或多核苷酸的方法。本发明还涉及一种反复循环诱变，洗牌和选择的方法，其允许蛋白质的体外或体内的定向分子进化。版权所有（C）2007，JPO＆INPIT

4. 发明专利

JP2010178757A Oligonucleotide-mediated nucleic acid recombination 审中-公开
标题翻译：寡核苷酸介导的核酸重组
公开(公告)号：JP2010178757A
公开(公告)日：2010-08-19
申请号：JP2010095500
申请日：2010-04-16
申请人： Maxygen Inc , マキシジェン, インコーポレイテッド
发明人： CRAMERI ANDREAS , STEMMER WILLEM P C , MINSHULL JEREMY , BASS STEVEN H , WELCH MARK , NESS JON E , GUSTAFSSON CLAES , PATTEN PHILIP A
IPC分类号： C12N15/09 , C12N1/15 , C12N1/19 , C12N1/21 , C12N5/10 , C12Q1/68
摘要： PROBLEM TO BE SOLVED: To provide a method for recombining nucleic acids including homologous nucleic acids, families of gene shuffling oligonucleotides, their use in a recombination procedure, and a polymerase- and ligase-mediated recombination method. SOLUTION: There is provided a method for oligonucleotide-assisted shuffling of nucleic acids. These oligonucleotide-assisted approaches especially facilitate a family shuffling procedure and provide an substantially simplified shuffling protocol. The protocol can be used for forming a family-shuffled nucleic acid without isolating or cloning whole-length homologous nucleic acids. COPYRIGHT: (C)2010,JPO&INPIT
摘要翻译：要解决的问题：提供重组核酸的方法，包括同源核酸，基因改组寡核苷酸家族，其在重组过程中的用途，以及聚合酶和连接酶介导的重组方法。解决方案：提供了核酸的寡核苷酸辅助改组方法。这些寡核苷酸辅助方法特别促进了家族洗牌过程并提供了基本上简化的洗牌方案。该方案可用于形成家族洗牌的核酸而不分离或克隆全长同源的核酸。版权所有（C）2010，JPO＆INPIT

5. 发明专利

JP2009089710A Method and composition for polypeptide engineering 审中-公开
标题翻译：多肽工程的方法与组合
公开(公告)号：JP2009089710A
公开(公告)日：2009-04-30
申请号：JP2008306897
申请日：2008-12-01
申请人： Maxygen Inc , マキシジェン, インコーポレイテッド
发明人： PATTEN PHILLIP A , STEMMER WILLEM P C
IPC分类号： C12N15/09 , A61K38/45 , A61K48/00 , C07K14/005 , C07K14/435 , C07K14/47 , C07K14/545 , C07K14/56 , C07K16/00 , C07K19/00 , C12N7/00 , C12N9/02 , C12N9/10 , C12N9/12 , C12N9/38 , C12N9/86 , C12N15/10 , C12N15/52 , C12N15/64 , C12P21/02 , C12Q1/02 , C12Q1/37 , C12Q1/68 , C40B40/02 , G01N33/68
CPC分类号： C12N15/1031 , A61K38/45 , A61K48/00 , C07K14/43595 , C07K14/545 , C07K14/56 , C07K16/00 , C07K2317/565 , C07K2317/622 , C12N7/00 , C12N9/0069 , C12N9/1007 , C12N9/16 , C12N9/86 , C12N15/10 , C12N15/1027 , C12N15/1034 , C12N15/1037 , C12N15/1058 , C12N15/52 , C12N15/64 , C12N15/67 , C12N2795/14043 , C12N2795/14143 , C12Q1/6811 , C12Q1/6853 , C12Q1/686 , C40B40/02 , C40B40/08 , C40B50/06 , G01N33/68 , G01N33/6845
摘要： PROBLEM TO BE SOLVED: To provide a number of strategies for evolving a polypeptide through a recursive recombination method. SOLUTION: A method for evolving a protein encoded by a DNA substrate molecule contains the following steps: (a) a step to digest at least the first and the second DNA substrate molecules with a restriction endonuclease, wherein the first and the second substrate molecules are different from each other at least by one nucleotide; (b) a step to connect the mixture for producing a library of recombinant DNA molecules; (c) a step to screen or select the product of the step (b) by a desired characteristic; and (d) a step to recover the recombinant DNA substrate molecule encoding the evolved protein. COPYRIGHT: (C)2009,JPO&INPIT
摘要翻译：要解决的问题：提供通过递归重组方法进化多肽的许多策略。解决方案：用于产生由DNA底物分子编码的蛋白质的方法包括以下步骤：（a）用限制性内切核酸酶消化至少第一和第二DNA底物分子的步骤，其中第一和第二底物分子至少一个核苷酸彼此不同; （b）将混合物连接以产生重组DNA分子文库的步骤; （c）按所需特性筛选或选择步骤（b）的产物的步骤; 和（d）回收编码进化蛋白质的重组DNA底物分子的步骤。版权所有（C）2009，JPO＆INPIT

6. 发明专利

JP2004187694A Methods for generating polynucleotides having desired characteristics by repetitive selection and recombination 审中-公开
公开(公告)号：JP2004187694A
公开(公告)日：2004-07-08
申请号：JP2004101193
申请日：2004-03-30
申请人： Maxygen Inc , マキシジェン, インコーポレイテッド
发明人： STEMMER WILLEM P C , CRAMERI ANDREAS
IPC分类号： C12N15/09 , C07K14/435 , C07K14/46 , C07K14/545 , C07K16/00 , C12N9/38 , C12N9/86 , C12N15/10 , C12N15/52 , C12N15/64 , C12Q1/68 , C40B40/02 , H01L29/772 , H01L29/78 , H01L29/808 , H01L39/22
CPC分类号： C40B40/02 , C07K14/43595 , C07K14/545 , C07K16/00 , C07K2317/565 , C07K2317/622 , C12N9/2471 , C12N9/86 , C12N15/1027 , C12N15/1034 , C12N15/1037 , C12N15/1058 , C12N15/52 , C12N15/64 , C12Q1/68 , C12Q1/6811 , C12Y302/01023 , C12Y305/02006 , H01L39/228 , C12Q2525/179
摘要： PROBLEM TO BE SOLVED: To provide a method for generating a mutant DNA, RNA or a large library of protein and selecting a specific mutant for a desired object. SOLUTION: In this method, a selected polynucleotide sequence or population of selected polynucleotide sequences is generated, typically in the form of amplified and/or cloned polynucleotides, the selected polynucleotide sequences possess a desired phenotypic characteristic (e.g., encode a polypeptide, promote transcription of linked polynucleotides, bind a protein, and the like) which can be selected for. COPYRIGHT: (C)2004,JPO&NCIPI

7. 发明专利

JP2003033180A Mutagenesis of dna by random fragmentation and reassembly 有权
标题翻译：通过随机分解和重新组装DNA诱导
公开(公告)号：JP2003033180A
公开(公告)日：2003-02-04
申请号：JP2002206303
申请日：2002-07-15
申请人： Maxygen Inc , マキシジェン, インコーポレイテッド
发明人： STEMMER WILLEM P C , CRAMERI ANDREAS
IPC分类号： C12N15/09 , A61K38/00 , A61K39/395 , C07K14/435 , C07K14/545 , C07K16/00 , C12N9/38 , C12N9/86 , C12N15/00 , C12N15/10 , C12P21/08 , C12Q1/68 , C40B40/02 , G01N33/53 , G01N33/566
CPC分类号： C40B40/02 , C07K14/43595 , C07K14/545 , C07K16/00 , C07K2317/565 , C07K2317/622 , C12N9/2471 , C12N9/86 , C12N15/1027 , C12N15/1034 , C12N15/1037 , C12Q1/68 , C12Q1/6811 , C12Y302/01023 , C12Y305/02006 , C40B40/08 , C40B50/06
摘要： PROBLEM TO BE SOLVED: To provide a method for production a mutant protein, and a method for developing a readily searchable large scale library of sequence of a mutant nucleic acid. SOLUTION: A method for DNA reassembly after random fragmentation, and its application to mutagenesis of nucleic acid sequences by in vitro, or in vivo recombination is described. In particular, a method for the production of nucleic acid fragments or polynucleotides encoding mutant proteins is described. A method of repeated cycles of mutagenesis, shuffling and selection enables the directed molecular evolution in vitro or in vivo of proteins.
摘要翻译：要解决的问题：提供突变蛋白质的制备方法，以及开发易于搜索的突变核酸序列的大规模文库的方法。解决方案：描述了随机断裂后DNA重组的方法及其在核酸序列的体外或体内重组诱变中的应用。特别地，描述了用于生产编码突变蛋白的核酸片段或多核苷酸的方法。重复循环的突变，混洗和选择的方法使得蛋白质的体外或体内的定向分子进化。

8. 发明专利

JP2004254709A DNA MUTAGENESIS BY RANDOM FRAGMENTATION AND REASSEMBLY 审中-公开
公开(公告)号：JP2004254709A
公开(公告)日：2004-09-16
申请号：JP2004174720
申请日：2004-06-11
申请人： MAXYGEN INC
发明人： STEMMER WILLEM P C , CRAMERI ANDREAS
IPC分类号： C12N15/09 , A61K38/00 , A61K39/395 , C07K14/435 , C07K14/545 , C07K16/00 , C12N9/38 , C12N9/86 , C12N15/00 , C12N15/10 , C12P21/08 , C12Q1/68 , C12Q1/6811 , C40B40/02 , G01N33/53 , G01N33/566
摘要： PROBLEM TO BE SOLVED: To provide a method for generating a mutant protein and a developing method of a readily searchable large-scale library of a mutant nucleic acid sequence. SOLUTION: A method for DNA reassembly after random fragmentation, and its application to mutagenesis of nucleic acid sequence by in vitro or in vivo recombination is described. More particularly, the method is used for generation of nucleic acid fragments or polynucleotides encoding mutant proteins. Moreover, the method provides repeated cycles of mutagenesis, shuffling and selection enabling the directed molecular evolution in vitro or in vivo of proteins. COPYRIGHT: (C)2004,JPO&NCIPI

9. 发明专利

JP2003174881A MUTAGENESIS OF DNA BY RANDOM FRAGMENTATION AND REASSEMBLY 审中-公开
公开(公告)号：JP2003174881A
公开(公告)日：2003-06-24
申请号：JP2002365621
申请日：2002-12-17
申请人： MAXYGEN INC
发明人： STEMMER WILLEM P C , CRAMERI ANDREAS
IPC分类号： C12N15/09 , A61K38/00 , A61K39/395 , C07K14/435 , C07K14/545 , C07K16/00 , C12N9/38 , C12N9/86 , C12N15/00 , C12N15/10 , C12P21/08 , C12Q1/68 , C12Q1/6811 , C40B40/02 , G01N33/53 , G01N33/566
摘要： PROBLEM TO BE SOLVED: To provide a method for producing a mutant protein, and a method for developing a readily searchable large scale library of sequence of a mutant nucleic acid. SOLUTION: The method for reassembling DNA after random fragmentation and its application to mutagenesis of nucleic acid sequences by in vitro or in vivo recombination are described. In particular, a method for the production of nucleic acid fragments or polynucleotides encoding mutant proteins is described. The method of repeated cycles of mutagenesis, rearrangement and selection enables the in vitro or in vivo direct molecular evolution of proteins. COPYRIGHT: (C)2003,JPO

10. 发明专利

JP2001197895A METHOD AND COMPOSITION FOR CELL TECHNOLOGY AND METABOLISM TECHNOLOGY 失效
公开(公告)号：JP2001197895A
公开(公告)日：2001-07-24
申请号：JP2000379523
申请日：2000-12-13
申请人： MAXYGEN INC
发明人： MINSHULL JEREMY , STEMMER WILLEM P C
IPC分类号： C12N15/09 , C07K14/11 , C07K14/435 , C07K14/545 , C07K16/00 , C12N1/15 , C12N1/19 , C12N1/21 , C12N5/10 , C12N9/38 , C12N9/86 , C12N15/10 , C12N15/52 , C12N15/64 , C12Q1/02 , C12Q1/68 , C40B40/02
摘要： PROBLEM TO BE SOLVED: To provide a method for evolving a new metabolic pathway and increasing a bioprocess. SOLUTION: This method is method for evloving the new metabolic pathway comprising the process generally called circulative sequence recombination in this disclosure and increasing the bioprocess. The circulative sequence recombination necessitates to carry out the repetitive cycle of recombination and screening or selection to evolve individual gene, whole plasmid or virus, multigene cluster or even whole genome. The technics like this necessitates no wide range of analysis and calculation needed in the conventional method on the metabolism technology.

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