Agrawal Ankit, Brendel Volker P, Huang Xiaoqiu
Department of Computer Science, Iowa State University, Ames, IA 50011-1041, USA.
Int J Comput Biol Drug Des. 2008;1(4):347-67. doi: 10.1504/ijcbdd.2008.022207.
We evaluate various methods to estimate pairwise statistical significance of a pairwise local sequence alignment in terms of statistical significance accuracy and compare it with popular database search programs in terms of retrieval accuracy on a benchmark database. Results indicate that using pairwise statistical significance using standard substitution matrices is significantly better than database statistical significance reported by BLAST and PSI-BLAST, and that it is comparable and at times significantly better than SSEARCH. An application of pairwise statistical significance to empirically determine effective gap opening penalties for protein local sequence alignment using the widely used BLOSUM matrices is also presented.
我们从统计显著性准确性方面评估了各种估计两两局部序列比对的两两统计显著性的方法，并在基准数据库上，就检索准确性而言，将其与流行的数据库搜索程序进行了比较。结果表明，使用标准替换矩阵的两两统计显著性明显优于BLAST和PSI-BLAST报告的数据库统计显著性，并且与SSEARCH相当，有时甚至明显更好。还介绍了两两统计显著性在使用广泛使用的BLOSUM矩阵凭经验确定蛋白质局部序列比对的有效空位开放罚分方面的应用。
