Improvements And Extensions To The Blast Algorithms

Blast 算法的改进和扩展

• 批准号: 6843572
• 负责人: STEPHEN F ALTSCHUL
• 金额: --
• 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/6843572
• 关键词: abstracting; aminoacid; chemical substitution; computer program /software; computer system design /evaluation; information retrieval; molecular biology information system; statistics /biometry

The BLAST family of protein and DNA database search programs constitute one of the key services offered by the NCBI. These programs are currently run on NCBI servers about 70,000 times during a typical weekday. This project represents an ongoing effort to improve and extend the functionality of these programs. Efforts this year have focussed primarily on the use of compositionally adjusted amino acid substitution matrices with "Blastp", the program for comparing protein queries to protein databases. Preliminary results indicate that such score matrices are useful primarily for the comparison of sequences with similar lengths (less than a factor of two difference), and for sequences whose compositions are relatively similar, as measured by relative entropy. Algorithmically, we have needed to rewrite the heuristic for producing gapped alignments when the substitution matrix used is modified. This is due to the fact that the rescaling procedure employed for compositionally adjusted statistics essentially never produced longer alignments, whereas the new compositionally adjusted matrices frequently yield extended alignments.

蛋白质和DNA数据库搜索程序的BLAST家族构成了NCBI提供的关键服务之一。这些程序目前在NCBI服务器上运行，在典型的工作日中约70,000次。该项目代表了改善和扩展这些程序功能的持续努力。 今年的努力主要集中在使用“ BLASTP”的成分调整后的氨基酸取代矩阵，该计划是将蛋白质查询与蛋白质数据库进行比较的程序。初步结果表明，这种评分矩阵主要用于比较具有相似长度的序列（小于两个差异），而对于通过相对熵来衡量的组成相对相对相对相似的序列。从算法上讲，我们需要在修改所使用的替换矩阵时，需要重写启发式的启发式对齐。这是由于以下事实：针对成分调整的统计数据所采用的重新制定程序本质上从未产生更长的比对，而新的组合调整后的矩阵经常产生扩展的比对。