Second Generation DNA Sequence Management Tools

第二代 DNA 序列管理工具

• 批准号: 6912979
• 负责人: TODD M SMITH
• 金额: $ 19.2万
• 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 2005-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6912979
• 关键词: artificial intelligence; computer data analysis; computer program /software; computer system design /evaluation; data management; genotype; informatics; mathematical model; nucleic acid sequence

DESCRIPTION (provided by applicant): The human genome project spurred the development of high throughput technologies, especially in the area of DNA sequencing. Not only has this effort produced a draft of the human genome, it's catalyzed development of an entire industry based on DNA sequencing and genomics. Since these technologies produce enormous amounts of data they depend on bioinformatics programs for data management. Phrap, Cross_Match, RepeatMasker and Consed are four programs that played an integral role in the human genome project and became accepted as standard. However, as the technology for sequencing has evolved, so too, have the applications. These new applications include sequencing additional genomes, EST cluster analysis, and genotyping and they have highlighted the need to update standard bioinformatics programs to meet the current needs of a broader community. In this project we will re-engineer Phrap, Cross_Match and Repeat Masker to improve performance by optimizing these algorithms and developing a hierarchical data file to store and manipulate assembled sequence data. Phrap and Cross_Match will also be modified to use XML-formatted data allowing users to apply constraints to sequence assembly. Lastly, we will develop a new program to review, edit, and manipulate sequences, thus giving users unprecedented control over their data. PROPOSED COMMERCIAL APPLICATION: 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.

描述（由申请人提供）：人类基因组项目刺激了 高通量技术的发展，尤其是在DNA领域 测序。这种努力不仅产生了人类基因组草案，而且还 基于DNA测序和 基因组学。由于这些技术产生了大量的数据，因此 关于数据管理的生物信息学计划。 phrap，cross_match， 反复分子和Consed是四个程序，在 人类基因组项目，并被接受为标准。但是，作为 测序技术也在发展中，也有应用。这些新 应用包括测序其他基因组，EST群集分析和 基因分型，它们强调了需要更新标准生物信息学 满足更广泛社区的当前需求的计划。在这个项目中，我们 会重新设计phrap，cross_match和重复蒙版，以提高性能 优化这些算法并开发层次数据文件以存储 并操纵组装序列数据。 phrap和cross_match也将是 修改以使用XML形式的数据，使用户可以将约束应用于 序列组件。最后，我们将开发一个新程序来审查，编辑和 操纵序列，从而为用户提供对数据的前所未有的控制。 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。