1. Aligning protein sequence and analysing substitution pattern using a class-specific matrix
- Author
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Xiao Hui Liu, Wen Ke Ren, Hai Song Xu, and Xiao Qin Li
- Subjects
Models, Molecular ,Protein Conformation ,Molecular Sequence Data ,Structural alignment ,Sequence alignment ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Substitution matrix ,Matrix (mathematics) ,Protein sequencing ,Sequence Analysis, Protein ,Protein methods ,Amino Acid Sequence ,Multiple sequence alignment ,business.industry ,Computational Biology ,Proteins ,BLOSUM ,Pattern recognition ,General Medicine ,Crystallography ,Amino Acid Substitution ,Artificial intelligence ,General Agricultural and Biological Sciences ,business ,Sequence Alignment ,Algorithms ,Software - 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.
- Published
- 2010
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