Second Generation DNA Sequence Management Tools

描述（由申请人提供）：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 测序这项工作不仅绘制出了人类基因组草图， 催化了基于DNA测序的整个行业的发展， 基因组学由于这些技术产生了大量的数据， 数据管理的生物信息学项目。Phrap，Cross_Match， RepeatMasker和Consed是四个程序，在 人类基因组计划并被接受为标准。但随着 测序技术已经发展，应用也已经发展。这些新 应用包括测序额外的基因组，EST聚类分析， 基因分型，他们强调需要更新标准的生物信息学 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，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也将在 修改为使用XML格式的数据，允许用户将约束应用于 序列组装。最后，我们将开发一个新的程序来审查，编辑， 操纵序列，从而使用户能够前所未有地控制他们的数据。 拟定商业应用： Phrap在工业和学术界广泛用于涉及DNA序列的应用。 有超过100个商业站点将受益于Phrap的新版本，这些新版本支持增量汇编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额外的商业化可能性。

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.