SGER: Performance Studies for Indexing Genome Sequence Databases

SGER：索引基因组序列数据库的性能研究

• 批准号: 0228983
• 负责人: Sakti Pramanik
• 金额: $ 1.36万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-09-01 至 2004-02-29
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0228983&HistoricalAwards=false
• 关键词: SGER; Performance; Studies; Indexing; Genome

The volume of sequence data grows exponentially; its analysis is a comutational challenge. The ability to analyze the data does not keep pace with production. One of the central tasks it rapid sequence comparisons. Effective strategies require algorithms that are better than linear on the size of the database in order to address the problem. In order to get an idea of how efficient various algorithms that index the database before comparing sequences are, a sensitive study of their utility against the major sequence database will be performed, considering exact and short mismatches. Indexing does improve performance so there is a possibility of identifying better ways to do it. An interdisciplinary graduate student is deeply involved in the work supported here.

序列数据量呈指数级增长；它的分析是一个计算挑战。 分析数据的能力跟不上生产的步伐。 中心任务之一是快速序列比较。 有效的策略需要比数据库大小线性更好的算法来解决问题。 为了了解在比较序列之前索引数据库的各种算法的效率如何，将针对主要序列数据库对其效用进行敏感研究，同时考虑精确和短的不匹配。 索引确实可以提高性能，因此有可能找到更好的方法来做到这一点。一名跨学科研究生深入参与了这里支持的工作。