SECOND GENERATION OF DNA SEQUENCE MANAGEMENT TOOLS

第二代 DNA 序列管理工具

• 批准号: 6211967
• 负责人: TODD M SMITH
• 金额: $ 9.82万
• 依托单位: GEOSPIZA, INC.
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-08-01 至 2001-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6211967
• 关键词: computer data analysis; computer program /software; computer system design /evaluation; data management; informatics; mathematical model; nucleic acid sequence

The tremendous amounts of sequence data made available in recent time have increased the need to re-engineer existing bioinformatics algorithms for better performance. Our ability to organize human and mouse genomic, cDNA, and EST (expressed sequence tag) data, rapidly assemble microbial genomes, and compare sequences within and between organisms depends on programs that can operate on large amounts of data and be easily incorporated into scientific applications. In the case of the popular assembly program Phrap (P. Green, unpublished), performance improvements include the ability to perform incremental assemblies, where new sequence data are added to already assembled sequences, better memory management to accommodate larger data sets, and running the algorithm as a parallel process to reduce assembly times. Further Improvements include developing an API (Application Programming Interface) so that Phrap can be better incorporated into bioinformatics applications. In this project a prototype of Phrap will be developed that performs incremental assemblies and has improved memory management. New versions of Phrap will be structured to run as parallel processes. Finally, we will develop specifications for an API and an XML-DTD (eXtensible Markup Language - Data Type Definition) that will allow Phrap to be more efficiently incorporated into bioinformatics applications. PROPOSED COMMERCIAL APPLICATIONS: Phrap is widely used in industry and academia for applications involving DNA sequences. There are over 100 commercial sites that would benefit from new versions of Phrap that support incremental assemblies and utilize computer resources better. An API for Phrap will encourage application development creating additional commercialization possibilities for algorithm and application developers.

最近提供的大量序列数据增加了重新设计现有的生物信息学算法以提高性能的需求。我们组织人类和小鼠基因组，cDNA和EST（表达序列标签）数据，迅速组装微生物基因组的能力，并比较生物体内部和生物之间的序列取决于可以在大量数据上操作并轻松纳入科学应用程序的程序。对于流行的组装程序Phrap（P. Green，未发表），性能改进包括执行增量组件的能力，其中将新的序列数据添加到已经组装的序列中，更好的内存管理以适应较大的数据集，并将算法作为平行过程以减少组装时间。进一步的改进包括开发API（应用程序编程界面），以便将Phrap更好地纳入生物信息学应用程序中。在此项目中，将开发出执行增量组件并改善内存管理的Phrap的原型。新版本的PHRAP将结构为并行过程运行。最后，我们将开发针对API和XML -DTD（可扩展的标记语言 - 数据类型定义）的规范，该规范将使Phrap更有效地整合到生物信息信息应用程序中。拟议的商业应用：PHRAP广泛用于行业和学术界，用于涉及DNA序列的应用。有100多个商业网站将从新版本的Phrap中受益，这些phrap支持增量组件并更好地利用计算机资源。 PHRAP的API将鼓励应用程序开发为算法和应用程序开发人员创造其他商业化可能性。