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1. 发明申请

US20090137505A1 Method for Predicting and Identifying Target mRnas Controlled By Functional Rnas and Method of Using the Same 审中-公开
标题翻译：通过功能性Rnas控制的目标mRnas的预测和识别方法及其使用方法
公开(公告)号：US20090137505A1
公开(公告)日：2009-05-28
申请号：US11992261
申请日：2006-09-20
申请人： Roberto Antonio Barrero , Takuro Tamura , Takashi Gojobori , Kazuho Ikeo , Tadashi Imanishi
发明人： Roberto Antonio Barrero , Takuro Tamura , Takashi Gojobori , Kazuho Ikeo , Tadashi Imanishi
IPC分类号： A61K31/7088 , G06F19/00 , G01N33/48 , C07H21/00
CPC分类号： C12Q1/6876 , C12N15/111 , C12N2310/14 , C12N2320/11 , C12N2330/10 , C12Q2600/158 , C12Q2600/178 , G16B15/00 , G16B20/00
摘要： It is intended to identify or estimate miRNAs and one or more target genes (target mRNAs) targeted thereby.A method of predicting or identifying miRNAs and one or more target mRNAs targeted thereby, which comprises calculating the most stable secondary structures of double-stranded RNAs, which can be formed by all partial sequences in all of the subject mRNAs with miRNAs, and the secondary structure energies thereof to thereby search for all partial sequences capable of having stable structures through the binding of miRNAs to mRNAs, and then calculating the most stable secondary structure, which can be formed by a subject partial sequence or regions in the vicinity of the subject partial sequence with partial sequences of the concerned mRNA, and the secondary structure energy thereof to thereby determine whether or not the subject partial sequence of the concerned mRNA has a structure capable of interacting with the miRNA.
摘要翻译：旨在鉴定或估计miRNA和靶向靶基因的一个或多个靶基因（靶mRNA）。一种预测或鉴定miRNA和由此靶向的一种或多种靶mRNA的方法，其包括计算双链RNA的最稳定的二级结构，其可以由所有与miRNA相关的所有受试者mRNA中的所有部分序列形成，并且次级结构能量，从而通过miRNA与mRNA的结合搜索能够具有稳定结构的所有部分序列，然后计算最稳定的二级结构，其可以由受试者部分序列或受试者部分附近的区域形成序列与相关mRNA的部分序列及其二级结构能，从而确定相关mRNA的受试者部分序列是否具有能够与miRNA相互作用的结构。

2. 发明授权

US5598350A Genetic motif extracting method and apparatus 失效
标题翻译：遗传基序提取方法及装置
公开(公告)号：US5598350A
公开(公告)日：1997-01-28
申请号：US339233
申请日：1994-11-10
申请人： Yuichi Kawanishi , Takashi Gojobori , Yoshio Tateno , Kazuho Ikeo , Masahito Kawai
发明人： Yuichi Kawanishi , Takashi Gojobori , Yoshio Tateno , Kazuho Ikeo , Masahito Kawai
IPC分类号： C12Q1/68 , G06F17/30 , G06F19/14 , G06F19/22 , G06F19/28 , G06F19/00 , G06F159/00
CPC分类号： G06F19/22 , C12Q1/68 , G06F19/14 , G06F19/28
摘要： A genetic motif extracting apparatus is adapted to extract a motif from genetic sequence information, where the motif has a regularity in a distinctive feature that specifies a genetic function. The genetic motif extracting apparatus includes a weight calculation unit for calculating a weight of each genetic sequence from a length of at least one branch of an evolution tree structure that is related to a plurality of genetic sequences, a score calculation unit for calculating a score that indicates a degree of similarity of sequence elements of the genetic sequences appearing at a site for each site of the genetic sequences using the weight calculated by the weight calculation unit, and a feature information extraction unit for extracting a part of the genetic sequence having the regularity in the distinctive feature as the motif based on the score calculated by the score calculation unit.
摘要翻译：遗传基序提取装置适于从遗传序列信息中提取基序，其中基序具有指定遗传功能的独特特征中的规律性。遗传基序提取装置包括：权重计算单元，用于从与多个遗传序列相关的进化树结构的至少一个分支的长度计算每个遗传序列的权重;计分计算单元，用于计算分数，表示使用由权重计算单元计算的权重，出现在遗传序列的每个位点的位点处的遗传序列的序列元件的相似程度，以及特征信息提取单元，用于提取具有规则性的一部分遗传序列在基于由分数计算单元计算的分数的图案的特征中。

3. 发明授权

US08510053B2 Method for modifying a property of a protein 有权
标题翻译：改变蛋白质性质的方法
公开(公告)号：US08510053B2
公开(公告)日：2013-08-13
申请号：US10933280
申请日：2004-09-03
申请人： Yosuke Nishio , Eiichiro Kimura , Yoshihiro Usuda , Kazuho Ikeo , Yoji Nakamura , Takashi Gojobori , Yutaka Kawarabayashi , Yumi Hino , Eiichi Hori , Jun Yamazaki
发明人： Yosuke Nishio , Eiichiro Kimura , Yoshihiro Usuda , Kazuho Ikeo , Yoji Nakamura , Takashi Gojobori , Yutaka Kawarabayashi , Yumi Hino , Eiichi Hori , Jun Yamazaki
IPC分类号： G01N33/50
CPC分类号： C12N9/88 , C12N9/00 , C12N9/0016 , C12N9/1205 , C12N15/1034 , C12N15/1089
摘要： The present invention relates to a method for modifying a property of a protein. The present invention also relates to a method for producing a protein which has a modified property, and a method for producing a microorganism which has a modified property. The present invention is useful in the field of microbial industrial production and the like.
摘要翻译：本发明涉及一种改变蛋白质性质的方法。本发明还涉及具有改性特性的蛋白质的制造方法，以及具有改性的微生物的制造方法。本发明在微生物工业生产等领域中是有用的。

4. 发明申请

US20100205204A1 HOMOLOGY RETRIEVAL SYSTEM, HOMOLOGY RETRIEVAL APPARATUS, AND HOMOLOGY RETRIEVAL METHOD 审中-公开
标题翻译：同位素检索系统，同源检索仪器和同步检索方法
公开(公告)号：US20100205204A1
公开(公告)日：2010-08-12
申请号：US12529506
申请日：2008-02-29
申请人： Takashi Gojobori , Kazuho Ikeo , Toshitsugu Okayama
发明人： Takashi Gojobori , Kazuho Ikeo , Toshitsugu Okayama
IPC分类号： G06F17/30
CPC分类号： G06F16/90344 , G16B30/00
摘要： A homology retrieval can be performed with higher accuracy than conventional technologies when comparing a query sequence with a target sequence, and retrieving a similar location in the target sequence. The sequence information of a query sequence and a genomic-scale target sequence is acquired, the acquired information is compressingly converted into a compressed query sequence and a compressed target sequence in each of which a homopolymer region including two or more consecutive identical bases is replaced with a single base of the bases, the two sequences are compared, and a refining search is performed for a compressed target partial sequence that matches the compressed query sequence in the compressed target sequence. For the refined compressed candidate sequence and the query sequence, based on the information on the number of consecutive identical bases in the each of the sequences before compression, the number of consecutive bases is compared between the two compressed sequences for each corresponding base, and the degree of similarity indicating homology of the candidate sequence with the query sequence is computed from a degree of match or a degree of mismatch in the number of consecutive bases. By ranking and selecting an arbitrary number of candidate sequences having relatively high homology with the query sequence from this degree of similarity, it is possible to avoid the influence of the number of consecutive identical bases in a homopolymer region, thereby performing a homology retrieval accurately.
摘要翻译：当将查询序列与目标序列进行比较时，可以以比传统技术更高的精度执行同源性检索，并且在目标序列中检索类似的位置。获取查询序列和基因组大小目标序列的序列信息，将所获取的信息压缩转换为压缩查询序列，并将压缩的目标序列分别包含两个或多个连续相同的碱基的均聚物区域替换为碱基的单个碱基，比较两个序列，并且对与压缩的目标序列中的压缩查询序列匹配的压缩目标部分序列进行精制搜索。对于经精制的压缩候选序列和查询序列，基于压缩前每个序列中连续相同碱基数的信息，对于每个对应的碱基，在两个压缩序列之间比较连续碱基数，从候选序列与查询序列的同源性的相似度的程度根据匹配度或连续基数的失配程度计算。通过从该相似度排序和选择与查询序列具有相对高同源性的任意数量的候选序列，可以避免在均聚物区域中连续相同碱基的数量的影响，从而准确地进行同源性检索。

5. 发明申请

US20050233308A1 Method for modifying a property of a protein 有权
标题翻译：改变蛋白质性质的方法
公开(公告)号：US20050233308A1
公开(公告)日：2005-10-20
申请号：US10933280
申请日：2004-09-03
申请人： Yosuke Nishio , Eiichiro Kimura , Yoshihiro Usuda , Kazuho Ikeo , Yoji Nakamura , Takashi Gojobori , Yutaka Kawarabayashi , Yumi Hino , Eiichi Hori , Jun Yamazaki
发明人： Yosuke Nishio , Eiichiro Kimura , Yoshihiro Usuda , Kazuho Ikeo , Yoji Nakamura , Takashi Gojobori , Yutaka Kawarabayashi , Yumi Hino , Eiichi Hori , Jun Yamazaki
IPC分类号： C12N15/09 , C12N1/21 , C12N9/00 , C12N15/10 , C12P21/02 , C12Q1/00 , G01N33/48 , G01N33/50 , G06F19/00
CPC分类号： C12N9/88 , C12N9/00 , C12N9/0016 , C12N9/1205 , C12N15/1034 , C12N15/1089
摘要： A property of a protein is modified by the following steps: (a) selecting 1000 or more genes from the genome of a first microorganism, and selecting 1000 or more genes from the genome of a second microorganism, wherein the genes from the first microorganism are orthologs to the genes from the second microorganism, and wherein the second microorganism is closely related to the first microorganism, but grows differently under at least one optimum growth condition when compared with the first microorganism, (b) comparing an amino acid sequence encoded by a gene from the first microorganism to an amino acid sequence encoded by the orthologous gene from the second microorganism, (c) detecting substitutions between the amino acid sequence encoded by a gene from the first microorganism and the amino acid sequence encoded by a gene from the second microorganism for each pair of orthologous genes, (d) compiling the detected amino acid substitutions for each amino acid substitution type, (e) calculating the frequency of each amino acid substitution type, wherein for each detected amino acid substitution type, a correction is made by subtracting the total number of substitution types which occur from the first microorganism to the second microorganism from the total number of the same substitution type which occurs in the reverse direction, or from the second microorganism to the first microorganism, (f) identifying and labelling the amino acid substitutions which occur at a high frequency as amino acid substitutions which are involved in said optimum growth condition, and (g) introducing one or more of the amino acid substitutions identified in (f) into the gene encoding the protein to modify a property of the protein.
摘要翻译：通过以下步骤修饰蛋白质的性质：（a）从第一微生物的基因组中选择1000个或更多个基因，并从第二微生物的基因组中选择1000个或更多个基因，其中来自第一个微生物的基因是与第二微生物的基因直系同源，其中第二微生物与第一微生物密切相关，但与第一微生物相比，在至少一个最佳生长条件下生长不同，（b）比较由第一微生物编码的氨基酸序列基因从第一微生物到由第二微生物的直系同源基因编码的氨基酸序列，（c）检测由第一微生物的基因编码的氨基酸序列与由第二微生物的基因编码的氨基酸序列之间的取代每对直系同源基因的微生物，（d）编码每个氨基酸取代类型的检测到的氨基酸取代，（e）cal 规定每个氨基酸取代型的频率，其中对于每个检测到的氨基酸取代类型，通过从相同的取代类型的总数中减去从第一微生物发生到第二微生物的替代类型的总数来进行校正（f）鉴定和标记高频发生的氨基酸取代作为参与所述最佳生长条件的氨基酸取代，和（g）将（f）中鉴定的一个或多个氨基酸取代引入编码蛋白质的基因中以改变蛋白质的性质。

6. 发明申请

US20050158742A1 Method for analyzing genome 审中-公开
标题翻译：分析基因组的方法
公开(公告)号：US20050158742A1
公开(公告)日：2005-07-21
申请号：US10992780
申请日：2004-11-22
申请人： Hajime Sugiyama , Yuichi Kawanishi , Yuji Kondo , Shigekazu Masumoto , Kazuho Ikeo
发明人： Hajime Sugiyama , Yuichi Kawanishi , Yuji Kondo , Shigekazu Masumoto , Kazuho Ikeo
IPC分类号： C12Q1/68 , G01N33/48 , G01N33/50 , G06F19/00
CPC分类号： G16B30/00 , G16B45/00
摘要： A method for analyzing a genome includes creating a first partial sequence composed of (n+1) pieces of partial sequences; creating a second partial sequence composed of (m+1) pieces of partial sequences; searching, in the first partial sequence, a partial sequence that prefix-matches with character information indicating bases of the second partial sequence; extracting match information including information on the partial sequences in the first partial sequence and the second partial sequence, and on a number of prefix-matched character information; creating a matrix display image based on the match information; and displaying the matrix display image.
摘要翻译：用于分析基因组的方法包括：创建由（n + 1）个部分序列构成的第一部分序列; 创建由（m + 1）个部分序列组成的第二部分序列; 在第一部分序列中搜索与指示第二部分序列的碱基的字符信息前缀匹配的部分序列; 提取包括关于第一部分序列和第二部分序列中的部分序列的信息的匹配信息，以及多个前缀匹配的字符信息; 基于匹配信息创建矩阵显示图像; 并显示矩阵显示图像。

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