| Title | Parameterized BLOSUM matrices for protein alignment |
| Creator | |
| Date Issued | 2015-05-01 |
| Source Publication | IEEE/ACM Transactions on Computational Biology and Bioinformatics
 |
| ISSN | 1545-5963 |
| Volume | 12Issue:3Pages:686-694 |
| Abstract | 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. |
| Keyword | Parameterized BLOSUM matrices Protein alignment Substitution matrix |
| DOI | 10.1109/TCBB.2014.2366126 |
| URL | View source |
| Language | 英语English |
| Scopus ID | 2-s2.0-84940370058 |
| Citation statistics | |
| Document Type | Journal article |
| Identifier | http://repository.uic.edu.cn/handle/39GCC9TT/9050 |
| Collection | Research outside affiliated institution |
| Affiliation | 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 |
| Recommended Citation 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. |
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