Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
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DOI：
10.1093/nar/25.17.3389
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发表时间：
1997-09-01
影响因子：
14.9
通讯作者：
Lipman, DJ
中科院分区：
文献类型：
--
作者：
Altschul, SF;Madden, TL;Lipman, DJ
BLAST程序是广泛使用的用于搜索蛋白质和DNA数据库的序列相似性的工具。对于蛋白质比较，本文所述的各种定义、算法和统计学改进允许BLAST程序的执行时间显著减少，同时增强它们对弱相似性的敏感性。用于触发字命中的延伸的新标准，与用于产生空位比对的新启发法相结合，产生以原始速度的大约三倍运行的空位BLAST程序，此外，还介绍了一种方法，用于将BLAST产生的统计学显著比对自动组合到位置特异性得分矩阵中，并使用该矩阵搜索数据库。所得到的位置特异性迭代BLAST（PSI-BLAST）程序以与空位BLAST大致相同的每次迭代速度运行，但在许多情况下对弱但生物相关的序列相似性更敏感。PSI-BLAST用于揭示BRCT超家族的几个新的和有趣的成员。
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities, A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original, In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix, The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.