Mathematically Rigorous Results In Sequence Matching.

序列匹配中严格的数学结果。

• 批准号: 8558104
• 负责人: John Spouge
• 金额: $ 30.37万
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8558104
• 关键词: Code; DNA; Databases; Individual; Letters; Methods; Retrieval; Scheme; Time; improved; next generation

The NCBI CoreTools now contains code from us, code that calculates to practical accuracies, and in less than 1 sec, all parameters of the modified Gumbel distribution (the Gumbel scale parameter, λ, pre-factor k, and finite-size correction). The BLAST group plans to use our faster calculations to generate the modified Gumbel parameters for several new DNA scoring schemes. The BLAST group have also implemented the new finite-size correction directly into their code, demonstrably improving BLAST sequence retrieval. The implementation even had unexpected benefits, such as improved retrieval from the Conserved Domain Database with rps-BLAST. In addition, biologists notice and find it irritating when an exact match to their query is not the highest-ranked hit in a sequence database. The new finite-size correction places identical matches more consistently at the top of the retrieval list than the old finite-size correction. We are now collaborating with Dr. Martin Frith in extending our methods to next-generation sequence matching, including frameshifts in DNA.

NCBI CoreTools现在包含我们的代码，可以在不到1秒的时间内计算出修改后的Gumbel分布的所有参数（Gumbel尺度参数，前因子k和有限大小校正）。BLAST小组计划使用我们更快的计算来为几个新的DNA评分方案生成修改后的Gumbel参数。BLAST小组还直接在他们的代码中实现了新的有限大小校正，明显改善了BLAST序列检索。该实现甚至有意想不到的好处，例如使用rps-BLAST改进了从保守域数据库中的检索。此外，生物学家注意到，当与他们的查询完全匹配的结果不是序列数据库中排名最高的结果时，他们会感到恼火。新的有限大小校正比旧的有限大小校正更一致地将相同的匹配放置在检索列表的顶部。我们现在正在与Martin Frith博士合作，将我们的方法扩展到下一代序列匹配，包括DNA中的移码。