Classification of Protein Sequences by a Novel Alignment-Free Method on Bacterial and Virus Families

Abstract

The classification of protein sequences provides valuable insights into bioinformatics. Most existing methods are based on sequence alignment algorithms, which become time-consuming as the size of the database increases. Therefore, there is a need to develop an improved method for effectively classifying protein sequences. In this paper, we propose a novel accumulated natural vector method to cluster protein sequences at a lower time cost without reducing accuracy. Our method projects each protein sequence as a point in a 250-dimensional space according to its amino acid distribution. Thus, the biological distance between any two proteins can be easily measured by the Euclidean distance between the corresponding points in the 250-dimensional space. The convex hull analysis and classification perform robustly on virus and bacteria datasets, effectively verifying our method.