ANALYSIS OF A BACILLUS-SUBTILIS GENOME FRAGMENT USING A COOPERATIVE COMPUTER-SYSTEM PROTOTYPE
ANALYSIS OF A BACILLUS-SUBTILIS GENOME FRAGMENT USING A COOPERATIVE COMPUTER-SYSTEM PROTOTYPE
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DOI：
10.1016/0378-1119(95)00636-k
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发表时间：
1995-01-01
期刊：
影响因子：
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通讯作者：
DANCHIN, A
中科院分区：
文献类型：
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作者：
MEDIGUE, C;MOSZER, I;DANCHIN, A
分析大规模测序项目产生的大量数据需要构建新的、复杂的计算机系统。这些系统应该能够管理生物数据以及它们的分析结果。它们还应该帮助用户选择最合适的方法，并将它们组合在一起，以解决全局分析任务。本文提出了一个为大规模序列数据分析提供环境的软件系统原型。作为实现这一目标的第一步，这种环境已经在枯草芽孢杆菌基因组测序项目中进行了测试。该系统整合了相关实体（基因、调控信号等）的描述性知识和方法学知识，包括一套可扩展的分析方法。在现有的两种面向对象模型的基础上，采用一种知识表示来实现该集成系统。此外，本原型提供了一个合适的用户界面，既可以同时显示由几种方法产生的结果，也可以与对象进行交互。我们在本文中提出了枯草芽孢杆菌基因组片段的分析，存在于数据库中，但没有注释。对片段中存在的基因进行注释，使我们能够将用于预测编码序列的几种方法的结果结合起来，并将其表征为包含一个隐藏噬菌体，即皮肤元件。皮肤元件的注释与染色体标准区域的比较表明，核苷酸序列的局部特征可以区分噬菌体和非噬菌体DNA序列。分析大规模测序项目所产生的海量数据需要建设新的。复杂的计算机系统。这些系统应该能够管理生物数据以及它们的分析结果。它们还应该帮助用户选择最合适的方法，并将它们组合在一起，以解决全局分析任务。本文提出了一个为大规模序列数据分析提供环境的软件系统原型。作为实现这个目标的第一步。这种环境已经在枯草芽孢杆菌基因组测序计划中进行了测试。该系统整合了相关实体（基因、调控信号等）的描述性知识和方法学知识，包括一套可扩展的分析方法。在现有的两种面向对象模型的基础上，采用一种知识表示来实现该集成系统。此外，本原型提供了一个合适的用户界面，既可以同时显示由几种方法产生的结果，也可以与对象进行交互。本文报道了枯草芽孢杆菌基因组片段的分析。存在于数据库中，但没有注释。对片段中存在的基因进行注释，使我们能够将用于预测编码序列的几种方法的结果结合起来，并将其表征为包含一个隐体噬菌体。皮肤元素。皮肤元件的注释与染色体标准区域的比较表明，核苷酸序列的局部特征可以区分噬菌体和非噬菌体DNA序列
Analysis of the huge volume of data generated by large scale sequencing projects requires the construction of new, sophisticated computer systems. These systems should be able to manage the biological data as well as the results of their analysis. They should also help the user to choose the most appropriate methods, and to string them together in order to solve a global analysis task. In this paper we present the prototype of a software system providing an environment for the analysis of large-scale sequence data. As a first step toward this end, this environment has been put to the test within the Bacillus subtilis genome sequencing project. This system integrates both the descriptive knowledge of the entities involved (genes, regulatory signals and the Like) and the methodological knowledge comprising an extensible set of analytical methods. A knowledge representation based on two existing object-oriented models is used to implement this integrated system. In addition, the present prototype provides a suitable user interface both for displaying simultaneously the results generated by several methods and for interacting with the objects. We present in this paper the analysis of a B. subtilis genome fragment, present in data libraries but not annotated. Annotation of the genes present in the fragment allowed us to combine the results of several methods used for predicting coding sequences, and to characterize it as comprising a cryptic phage, the skin element. Comparison between the annotation of the skin element and a standard region of the chromosome indicated that local features of the nucleotide sequence could discriminate between phage and non-phage DNA sequence.Analysis of the huge volume of data generated by large scale sequencing projects requires the construction of new. sophisticated computer systems. These systems should be able to manage the biological data as well as the results of their analysis. They should also help the user to choose the most appropriate methods and to string them together in order to solve a global analysis task. In this paper we present the prototype of a software system providing an environment for the analysis of large scale sequence data. As a first step toward this end. this environment has been put to the test within the Bacillus subtilis genome sequencing project. This system integrates both the descriptive knowledge of the entities involved (genes, regulatory signals and the like) and the methodological knowledge comprising an extensible set of analytical methods. A knowledge representation based on two existing object-oriented models is used to implement this integrated system. In addition, the present prototype provides a suitable user interface both for displaying simultaneously the results generated by several methods and for interacting with the objects. We present in this paper the analysis of a B. subtilis genome fragment. present in data libraries but not annotated. Annotation of the genes present in the fragment allowed us to combine the results of several methods used for predicting coding sequences, and to characterize it as comprising a cryptic phage. the skin element. Comparison between the annotation of the skin element and a standard region of the chromosome indicated that local features of the nucleotide sequence could discriminate between phage and non-phage DNA sequence