Pegasys: software for executing and integrating analyses of biological sequences.
Pegasys: software for executing and integrating analyses of biological sequences.
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DOI：
10.1186/1471-2105-5-40
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发表时间：
2004-04-19
影响因子：
3
通讯作者：
Ouellette BF
中科院分区：
文献类型：
--
作者：
Shah SP;He DY;Sawkins JN;Druce JC;Quon G;Lett D;Zheng GX;Xu T;Ouellette BF
我们介绍了Pegasys -一个灵活的，模块化的和可定制的软件系统，便于执行和数据集成从异构生物序列分析工具。Pegasys系统包括许多用于成对和多重序列比对、从头算基因预测、RNA基因检测、掩蔽基因组DNA中的重复序列的工具，以及用于数据库格式化和处理各种分析工具的原始输出的过滤器。我们引入了一种新的数据结构，用于创建序列分析的工作流程和一个统一的数据模型来存储其结果。该软件允许用户通过操作图形用户界面在运行时动态创建分析工作流。所有非串行相关分析都在计算集群上并行执行，以提高数据生成效率。Pegasys的统一数据模型和后端关系数据库管理系统允许将工作流程中包含的异构程序的结果集成并导出为通用特征格式，以便在GFF依赖的工具中进行进一步分析，或将GAME XML导入Apollo基因组编辑器。模块化的设计允许新的工具被添加到系统中，而程序员的开销很小。数据库应用程序编程接口允许通过SQL查询对存储在后端的数据进行编程访问。Pegasys系统使生物学家和生物信息学家能够创建和管理序列分析工作流程。该软件在开放源代码GNU通用公共许可证下发布。所有的源代码和文档都可以在下载。
We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at .
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