Improvements and Extensions to the BLAST Algorithms

BLAST 算法的改进和扩展

• 批准号: 8558100
• 负责人: STEPHEN F ALTSCHUL
• 金额: $ 17.79万
• 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/8558100
• 关键词: Algorithms; DNA Databases; Databases; Family; Process; Protein Databases; Protein Structure Initiative; Running; Services; Time; improved; programs; protein profiling; web site

This project had two central focuses this year: 1) The PSI-BLAST program greatly increases the sensitivity of protein-database similarity searches. It constructs a multiple alignment from significant similarities to a query sequence, derives a "profile" from this alignment, and searches the database anew, using the profile as a query. We sought to accelerate this process by performing an initial search not to a standard sequence database, but rather to a database of pre-constructed protein profiles, such as the Conserved Domain Database (CDD), maintained by NCBI. When any hits were found, the profiles constructed after this fast initial search were, on average, as sensitive in finding sequences related to the query as were profiles constructed after multiple rounds of PSI-BLAST searching, requiring much more time. The program for this purpose, Domain Enhanced Lookup Time Accelerated BLAST (DELTA-BLAST) has been made available on the NCBI web site. 2) We continued to investigate the means for decreasing the number of false positive hits in PSI-BLAST searches by means of alignment trimming, to decrease the chance of profile corruption due to homologous over-extensions.

今年该项目有两个中心重点： 1）PSI-BLAST程序大大提高了灵敏度 蛋白质数据库相似性搜索。 它构建了一个 与查询的显着相似性的多重对齐 序列，从该比对中得出“概况”，并且 使用配置文件作为查询重新搜索数据库。 我们试图通过执行以下操作来加速这一过程 初始搜索不是针对标准序列数据库，而是 而不是预先构建的蛋白质谱数据库， 例如保守域数据库（CDD），维护 由 NCBI 提供。 当发现任何命中时，就会构建配置文件 经过这种快速的初步搜索后，平均而言，敏感度 查找与查询相关的序列以及配置文件 经过多轮 PSI-BLAST 搜索后构建， 需要更多的时间。 为此目的而制定的计划， 域增强查找时间加速 BLAST (DELTA-BLAST) 已在 NCBI 网站上提供。 2）我们继续研究减少 PSI-BLAST 搜索中误报命中的数量 对齐修剪，以减少轮廓的机会 由于同源过度扩展而导致腐败。