Improvements And Extensions To The Blast Algorithms

BLAST家族的蛋白质和DNA数据库搜索程序构成了NCBI提供的关键服务之一。这些程序目前在NCBI服务器上运行约70，000次，在一个典型的工作日。这个项目代表了一个持续的努力，以改善和扩展这些程序的功能。 今年的努力主要集中在使用组成调整的氨基酸取代矩阵与“Blastp”，程序比较蛋白质查询蛋白质数据库。初步结果表明，这样的评分矩阵是有用的，主要用于比较序列具有相似的长度（小于两个差异的一个因素），并为序列的组成是相对相似的，作为测量的相对熵。从数学上讲，当使用的替换矩阵被修改时，我们需要重写产生空位比对的启发式。这是由于这样一个事实，即用于成分调整统计的重新缩放过程基本上从来没有产生更长的对齐，而新的成分调整矩阵经常产生扩展的对齐。

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.