title: Aligning protein sequence and analysing substitution pattern using a class-specific matrix.
abstract: Aligning protein sequences using a score matrix has became a routine but valuable method in modern biological research. However, alignment in the 'twilight zone' remains an open issue. It is feasible and necessary to construct a new score matrix as more protein structures are resolved. Three structural class-specific score matrices (all-alpha, all-beta and alpha/beta) were constructed based on the structure alignment of low identity proteins of the corresponding structural classes. The class-specific score matrices were significantly better than a structure-derived matrix (HSDM) and three other generalized matrices (BLOSUM30, BLOSUM60 and Gonnet250) in alignment performance tests. The optimized gap penalties presented here also promote alignment performance. The results indicate that different protein classes have distinct amino acid substitution patterns, and an amino acid score matrix should be constructed based on different structural classes. The class-specific score matrices could also be used in profile construction to improve homology detection.
authors.affiliation: College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
authors.forename: Hai Song
authors.initials: HS
authors.lastname: Xu
authors.forename: Wen Ke
authors.initials: WK
authors.lastname: Ren
authors.forename: Xiao Hui
authors.initials: XH
authors.lastname: Liu
authors.forename: Xiao Qin
authors.initials: XQ
authors.lastname: Li
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D019295:Computational Biology / Q000379:methods; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software
chemical_list: D011506:Proteins