Iterative Hybrid Alignment: Improving the Sensitivity of Biological Database Searches

迭代混合比对：提高生物数据库搜索的灵敏度

• 批准号: 0317335
• 负责人: Ralf Bundschuh
• 金额: $ 35.01万
• 依托单位: Ohio State University Research Foundation -DO NOT USE
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-09-01 至 2007-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0317335&HistoricalAwards=false
• 关键词: Iterative; Hybrid; Alignment; Improving; Sensitivity

A grant has been awarded to Ohio State University to build a computer program that will allow researchers to find matches or matching areas in genetic sequences even when those matches are very weak. The degree of matching and the specifics of that matching among protein sequences of different organisms is central to understanding evolution and fundamental biological processes common to all organisms. As the databases of sequence data become larger and questions become more far reaching, the need for smarter search and matching algorithms becomes crucial. In this project, the PI's will develop a highly sensitive search algorithm for identifying homologies even in cases in which the actual homologies are very weak. The algorithm proposed makes much better use than current algorithms of the calculated statistical costs of insertions and deletions as they vary across the sequence. The first implementation is proposed as a redesign of PSI-BLAST but it amounts to a complete replacement of the core algorithm of that popular protein sequence search algorithm. There will also be significant changes in the peripheral functions as well. This is a new tool that will have impacts on research involving matching algorithms in general as well as within the genomics/proteomics community.

俄亥俄州立大学获得了一笔拨款，用于构建一个计算机程序，使研究人员能够在基因序列中找到匹配或匹配区域，即使这些匹配非常弱。不同生物体蛋白质序列之间的匹配程度和匹配细节对于理解所有生物体共有的进化和基本生物过程至关重要。随着序列数据的数据库变得越来越大，问题变得越来越深远，对更智能的搜索和匹配算法的需求变得至关重要。在这个项目中，PI 将开发一种高度敏感的搜索算法，即使在实际同源性非常弱的情况下也能识别同源性。 所提出的算法比当前算法更好地利用了插入和删除的计算统计成本，因为它们在序列中各不相同。第一个实现被提议为 PSI-BLAST 的重新设计，但它相当于完全替换了流行的蛋白质序列搜索算法的核心算法。 外围功能也将发生重大变化。 这是一种新工具，将对涉及一般匹配算法以及基因组学/蛋白质组学界的研究产生影响。