Phylogenetic analysis of protein sequences based on distribution of length about common sub-string

Abstract

Up to now, various approaches for phylogenetic analysis have been developed. Almost all of them put stress on analyzing nucleic acid sequences or protein primary sequences. In this paper, we propose a new sequence distance for efficient reconstruction of phylogenetic trees based on the distribution of length about common sub-sequences between two sequences. We describe some applications of this method, which not only show the validity of the method, but also suggest a number of novel phylogenetic insights.

Fig. 1

The phylogenetic tree is constructed by our method HCS(A, B). The proteomic sequence is a concatenation of all the known amino acid sequences for an organism, also with delimiters. Our phylogenetic tree can be obtained at any ionic strength, temperature, time

Fig. 2

The phylogenetic tree is based on the distance of structural characteristic vector in Dai et al. . The proteomic sequence is a concatenation of all the known amino acid sequences for an organism, also with delimiters. The phylogenetic tree can be obtained at any ionic strength, temperature, time

Fig. 3

The phylogenetic tree for 26 spike proteins is constructed based on our method HCS(A, B). The proteomic sequence is a concatenation of all the known amino acid sequences for an organism, also with delimiters. Our phylogenetic tree can be obtained at any ionic strength, temperature, time