Substitution Matrices of Residue Triplets Derived from Protein Blocks.
文献类型：期刊论文
| 作者 | Liu X(刘鑫) ; Zhao YP(赵亚溥)
|
| 刊名 | Journal of Computational Biology
 |
| 出版日期 | 2010 |
| 卷号 | 17期号:12页码:1679 |
| 通讯作者邮箱 | yzhao@imech.ac.cn |
| 关键词 | hydrophobicity, sequence alignment, twilight zone. |
| ISSN号 | 1066-5277 |
| 通讯作者 | 赵亚溥 |
| 合作状况 | 其它 |
| 中文摘要 | In protein sequence alignment, residue similarity is usually evaluated by substitution matrix, which scores all possible exchanges of one amino acid with another. Several matrices are widely used in sequence alignment, including PAM matrices derived from homologous sequence and BLOSUM matrices derived from aligned segments of BLOCKS. However, most matrices have not addressed the high-order residue-residue interactions that are vital to the bioproperties of protein.With consideration for the inherent correlation in residue triplet, we present a new scoring scheme for sequence alignment. Protein sequence is treated as overlapping and successive 3-residue segments. Two edge residues of a triplet are clustered into hydrophobic or polar categories, respectively. Protein sequence is then rewritten into triplet sequence with 2 · 20 · 2 = 80 alphabets. Using a traditional approach, we construct a new scoring scheme named TLESUMhp (TripLEt SUbstitution Matrices with hydropobic and polar information) for pairwise substitution of triplets, which characterizes the similarity of residue triplets. The applications of this matrix led to marked improvements in multiple sequence alignment and in searching structurally alike residue segments. The reason for the occurrence of the ‘‘twilight zone,’’ i.e., structure explosion of lowidentity sequences, is also discussed. |
| 学科主题 | 交叉与边缘领域的力学 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000285184700005 |
| 公开日期 | 2010-12-21 |
| 源URL | [http://dspace.imech.ac.cn/handle/311007/43254]  |
| 专题 | 力学研究所_非线性力学国家重点实验室 |
| 推荐引用方式 GB/T 7714 | Liu X,Zhao YP. Substitution Matrices of Residue Triplets Derived from Protein Blocks.[J]. Journal of Computational Biology,2010,17(12):1679. |
| APA | 刘鑫,&赵亚溥.(2010).Substitution Matrices of Residue Triplets Derived from Protein Blocks..Journal of Computational Biology,17(12),1679. |
| MLA | 刘鑫,et al."Substitution Matrices of Residue Triplets Derived from Protein Blocks.".Journal of Computational Biology 17.12(2010):1679. |
入库方式： OAI收割
来源：力学研究所
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