PTGAC Model: A machine learning approach for constructing phylogenetic tree to compare protein sequences

Abstract

This work proposes a machine learning-based phylogenetic tree generation model based on agglomerative clustering (PTGAC) that compares protein sequences considering all known chemical properties of amino acids. The proposed model can serve as a suitable alternative to the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), which is inherently time-consuming in nature. Initially, principal component analysis (PCA) is used in the proposed scheme to reduce the dimensions of 20 amino acids using seven known chemical characteristics, yielding 20 TP (Total Points) values for each amino acid. The approach of cumulative summing is then used to give a non-degenerate numeric representation of the sequences based on these 20 TP values. A special kind of three-component vector is proposed as a descriptor, which consists of a new type of non-central moment of orders one, two, and three. Subsequently, the proposed model uses Euclidean Distance measures among the descriptors to create a distance matrix. Finally, a phylogenetic tree is constructed using hierarchical agglomerative clustering based on the distance matrix. The results are compared with the UPGMA and other existing methods in terms of the quality and time of constructing the phylogenetic tree. Both qualitative and quantitative analysis are performed as key assessment criteria for analyzing the performance of the proposed model. The qualitative analysis of the phylogenetic tree is performed by considering rationalized perception, while the quantitative analysis is performed based on symmetric distance (SD). On both criteria, the results obtained by the proposed model are more satisfactory than those produced earlier on the same species by other methods. Notably, this method is found to be efficient in terms of both time and space requirements and is capable of dealing with protein sequences of varying lengths.