Second Generation DNA Sequence Management Tools

描述(申请人提供)：人类基因组计划刺激了 高通量技术的发展，特别是在DNA领域 测序。这一努力不仅产生了人类基因组的草图，它还 促进了整个行业的发展，基于DNA测序和 基因组学。由于这些技术产生了海量数据，因此它们依赖于 关于用于数据管理的生物信息学程序。Phrap，Cross_Match， RepeatMasker和Consed是四个在 人类基因组计划，并被接受为标准。然而，由于 测序技术已经发展，应用程序也是如此。这些新的 应用包括对其他基因组进行测序，EST聚类分析，以及 他们强调了更新标准生物信息学的必要性 计划，以满足更广泛社区的当前需求。在这个项目中，我们 将重新设计Phrap、Cross_Match和Repeat Masker以通过以下方式提高性能 优化这些算法，并开发一个分层数据文件来存储 并操纵组装的序列数据。Phrap和Cross_Match也将 修改为使用XML格式的数据，允许用户将约束应用于 序列装配。最后，我们将开发一个新的程序来查看、编辑和 操纵序列，从而使用户能够前所未有地控制他们的数据。 建议的商业应用： Phrap在工业和学术界涉及DNA序列的应用中被广泛使用。有100多个商业网站将受益于支持增量汇编并更好地利用计算机资源的新版本的Phrap。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更多的商业化可能性。

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.