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Substitution Matrices of Residue Triplets Derived from Protein Blocks.
Liu X(刘鑫); Zhao YP(赵亚溥)
Source PublicationJournal of Computational Biology
AbstractIn 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.
Keywordhydrophobicity Sequence Alignment Twilight Zone.
Subject Area交叉与边缘领域的力学
Indexed BySCI
WOS IDWOS:000285184700005
Citation statistics
Cited Times:3[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Corresponding AuthorZhao YP(赵亚溥)
Recommended Citation
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.
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