Affiliation:
1. College of Science, Northwest A&F University, Yangling 712100, China
Abstract
Background:
The comparison of the protein sequences is an important research filed in
bioinformatics. Many alignment-free methods have been proposed.
Objective:
In order to mining the more information of the protein sequence, this study focus on a
new alignment-free method based on physiochemical properties of amino acids.
Methods:
Average physiochemical value (Apv) has been defined. For a given protein sequence, a
2D curve was outlined based on Apv and position of the amino acid, and there is not loop and
intersection on the curve. According to the curve, the similarity/dissimilarity of the protein
sequences can be analyzed.
Results and Conclusion:
Two groups of protein sequences are taken as examples to illustrate the
new methods, the protein sequences can be classified correctly, and the results are highly
correlated with that of ClustalW. The new method is simple and effective.
Funder
Fundamental research funds for the central universities
National Natural Science Foundation of China
Publisher
Bentham Science Publishers Ltd.
Subject
Computational Mathematics,Genetics,Molecular Biology,Biochemistry
Cited by
3 articles.
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