SECOND GENERATION OF DNA SEQUENCE MANAGEMENT TOOLS

近年来，大量的序列数据已经增加了重新设计现有生物信息学算法以获得更好性能的需求。我们组织人类和小鼠基因组、cDNA和EST（表达序列标签）数据、快速组装微生物基因组以及在生物体内和生物体之间比较序列的能力取决于能够对大量数据进行操作并易于纳入科学应用的程序。在流行的汇编程序Phrap（P.绿色，未发表）的情况下，性能改进包括执行增量汇编的能力，其中新的序列数据被添加到已经汇编的序列，更好的内存管理，以适应更大的数据集，并运行算法作为一个并行过程，以减少汇编时间。进一步的改进包括开发一个API（应用程序编程接口），使Phrap可以更好地纳入生物信息学应用程序。在这个项目中，将开发一个Phrap的原型，它可以执行增量汇编并改进内存管理。Phrap的新版本将被构造为作为并行进程运行。最后，我们将开发一个API和一个XML-DTD（可扩展标记语言-数据类型定义），这将使Phrap更有效地纳入生物信息学应用的规范。拟议的商业应用：Phrap广泛用于工业和学术界，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。

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 In the case of the popular assembly program Phrap (P. Green, unpublished), performance improvements include the ability to perform incremental assemblies, where new sequence data are added to already assembled sequences, better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.