Simplification of Protein Sequence and Alignment?-free Sequence Analysis
- VernacularTitle:蛋白质序列复杂性简化与非比对序列分析
- Author:
Jing LI
;
Fengbo LI
;
Wei WANG
- Publication Type:Journal Article
- Keywords:
alignment-free comparison, grouping of amino acids, simplification of protein sequence
- From:
Progress in Biochemistry and Biophysics
2006;0(12):-
- CountryChina
- Language:Chinese
-
Abstract:
Alignment-free comparison is a recently developed method for sequence alignment, which has high computational efficiency and suitable to the low identical sequences. Alignment-free comparison was successfully applied in the DNA analysis. However, the accuracy of analysis is not high when it was applied in protein analysis because the complexity of protein is larger than DNA by consisting of 20 types of residues. Thus, residues are clustered into a few groups based on their similarity of physicochemical features. Using such simplified alphabets, the complexity of protein sequences is reduced and at the same time the key information encoded in the sequences remains. Therefore, the accuracy of alignment-free comparison is improved.
