Simulation sutudy for high-speed DNA sequencing

高速DNA测序的模拟研究

• 批准号: 07680743
• 负责人: NOGUCHI Yohio
• 金额: $ 1.09万
• 依托单位: SAGA University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 1995
• 资助国家: 日本
• 起止时间: 1995 至 1997
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-07680743/
• 关键词: DNA sequencing; DNA probe; hybirdization; genatic algorithms; oligonucleotides; SBH method; chromosomr sorter; fluorescence profile; オリゴヌクレオチド・パネル; クローン・ライブラリー; ハイブリダイズ; 染色体; 自己組織化マップ; クラスタリング; クローン・パネル; 塩基配列決定法; ニューラル・ネットワーク; 遺伝的アルブリズム

An unknown DNA sequence is called a target DNA.A panel on which all possible sequences of oligonucleotide probes (ONPs) of a certain length are arranged in mesh-like form is called an oligonucleotide-panel and each ONP is called a DNA probe. Computer handling method based on hybridization information between the target DNA and DNA probes is called a sequencing by hybridization method (SBH in abbreviation) hereafter. Applicability of a genetic algorithm to the SBH method has been prved by this studies under the following condetions. Condetion 1) There is no mismatch between the DNA probes and the target DNA.Condition 2) Multiple hybridizations of certain probes to the target DNA are allowed. Conditon 3) The target DNA is not separated into two fragments.Computer simulation of the algorithm for DNA sequencing reveals the following facts. 1) Longer bases in ONP is more useful, but too much longer bases requires much longer computation time. 2) The method can be applied to more than 10K-bases segment of DNA.Improvement of the algorithm for handling mismatch-free hybridezations will be a future problem.

未知的DNA序列称为靶DNA。一定长度的所有可能的寡核苷酸探针(ONP)序列以网状形式排列的面板称为寡核苷酸面板，每个ONP称为DNA探针。根据靶DNA和DNA探针之间的杂交信息进行计算机处理的方法以下称为杂交测序法(SBH)。本研究在下列条件下证明了遗传算法对SBH方法的适用性。条件1)DNA探针与靶DNA之间不存在不匹配。条件2)某些探针与靶DNA多次杂交是允许的。条件3)目标DNA没有被分成两个片段。对DNA测序算法的计算机模拟揭示了以下事实。1)在ONP中，更长的基数更有用，但太长的基数需要更长的计算时间。2)该方法可应用于10K碱基以上的DNA片段，无错配杂交算法的改进将是未来的研究方向。

项目成果

H.Douzono, S.Hara, S.Kawamoto, & Y.Noguchi: "An application of genetic algorithm to clustering of chromosome fluorescence prfile" Workshop on Evolut.Computat. : Tenth Australian Joint Conf.on Artificial Intelligence. (1997)

H.Douzono、S.Hara、S.Kawamoto、

野口義夫: "染色体分析と分取" 臨床検査. 41・10. 1167-1169 (1997)

Yoshio Noguchi：“染色体分析和分选”临床检查41・10（1997）。

原重臣,堂薗浩,野口義夫: "染色体蛍光プロフィールの自己組織化マップによるクラスタリング" Cytometry Research. 7・2. 57-62 (1997)

Shigeomi Hara、Hiroshi Dozono、Yoshio Noguchi：“使用自组织图谱对染色体荧光图谱进行聚类”，细胞计数研究 7・2。

H.Donzono,S.Hara,S.Kawamoto,Y.Noguchi: "An application of genetic algorithm to clustering of chromosome fluoresance profile" Proc.of 10-th Australian. Joint Cont in AI. (1998)

H.Donzono、S.Hara、S.Kawamoto、Y.Noguchi：“遗传算法在染色体荧光谱聚类中的应用”第 10 期澳大利亚论文集。

S.Hara,H.Douzono,S.Eishima,Y.Noguchi: "Clustering of chromosome flucresance profiles by self-organizing map using chromosome Dhysical models" Proc.3rd IEEE SINBS. (to be published). (1998)

S.Hara、H.Douzono、S.Eishima、Y.Noguchi：“使用染色体 Dhysical 模型通过自组织图对染色体荧光谱进行聚类”Proc.3rd IEEE SINBS。