A 2D Non-degeneracy Graphical Representation of Protein Sequence and Its Applications

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.