Parameterized BLOSUM matrices for protein alignment

doi:10.1109/TCBB.2014.2366126

科研成果详情

题名	Parameterized BLOSUM matrices for protein alignment
作者	Song，Dandan 1; Chen，Jiaxing 2; Chen，Guang 1; Li，Ning 3; Li，Jin 1; Fan，Jun 5; Bu，Dongbo 4; Li，Shuai Cheng 3
发表日期	2015-05-01
发表期刊	IEEE/ACM Transactions on Computational Biology and Bioinformatics
ISSN/eISSN	1545-5963
卷号	12 期号:3 页码:686-694
摘要	Protein alignment is a basic step for many molecular biology researches. The BLOSUM matrices, especially BLOSUM62, are the de facto standard matrices for protein alignments. However, after widely utilization of the matrices for 15 years, programming errors were surprisingly found in the initial version of source codes for their generation. And amazingly, after bug correction, the "intended" BLOSUM62 matrix performs consistently worse than the "miscalculated" one. In this paper, we find linear relationships among the eigenvalues of the matrices and propose an algorithm to find optimal unified eigenvectors. With them, we can parameterize matrix BLOSUMx for any given variable x that could change continuously. We compare the effectiveness of our parameterized isentropic matrix with BLOSUM62. Furthermore, an iterative alignment and matrix selection process is proposed to adaptively find the best parameter and globally align two sequences. Experiments are conducted on aligning 13, 667 families of Pfam database and on clustering MHC II protein sequences, whose improved accuracy demonstrates the effectiveness of our proposed method.
关键词	Parameterized BLOSUM matrices Protein alignment Substitution matrix
DOI	10.1109/TCBB.2014.2366126
URL	查看来源
语种	英语English
Scopus入藏号	2-s2.0-84940370058
引用统计	被引频次：19[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	https://repository.uic.edu.cn/handle/39GCC9TT/9050
专题	个人在本单位外知识产出
作者单位	1.Beijing Engineering Research Center, High Volume Language Information Processing and Cloud Computing Applications, School of Computer Science and Technology, Beijing Institute of Technology,Beijing,100081,China 2.Department of Computer Science, University of Missouri,Columbia,65211,United States 3.City University of Hong Kong, Department of Computer Science,Kowloon,Hong Kong 4.Key Lab of Intelligence Information Processing, Institute of Computing Technology, Chinese Academy of Sciences,Beijing,100190,China 5.Department of Statistics, University of Wisconsin-Madison,Madison,53706,United States
推荐引用方式 GB/T 7714	Song，Dandan,Chen，Jiaxing,Chen，Guanget al. Parameterized BLOSUM matrices for protein alignment[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015, 12(3): 686-694.
APA	Song，Dandan., Chen，Jiaxing., Chen，Guang., Li，Ning., Li，Jin., .. & Li，Shuai Cheng. (2015). Parameterized BLOSUM matrices for protein alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(3), 686-694.
MLA	Song，Dandan,et al."Parameterized BLOSUM matrices for protein alignment". IEEE/ACM Transactions on Computational Biology and Bioinformatics 12.3(2015): 686-694.