D-graph clusters flaviviruses and β-coronaviruses according to their hosts, disease type and human cell receptors

Abstract

MotivationThere is a need for rapid and easy to use, alignment free methods to cluster large groups of protein sequence data. Commonly used phylogenetic trees based on alignments can be used to visualize only a limited number of protein sequences. DGraph, introduced here, is a dynamic programming application developed to generate 2D-maps based on similarity scores for sequences. The program automatically calculates and graphically displays property distance (PD) scores based on physico-chemical property (PCP) similarities from an unaligned list of FASTA files. Such "PD-graphs" show the interrelatedness of the sequences, whereby clusters can reveal deeper connectivities. ResultsPD-Graphs generated for flavivirus (FV), enterovirus (EV), and coronavirus (CoV) sequences from complete polyproteins or individual proteins are consistent with biological data on vector types, hosts, cellular receptors and disease phenotypes. PD-graphs separate the tick- from the mosquito-borne FV, clusters viruses that infect bats, camels, seabirds and humans separately and the clusters correlate with disease phenotype. The PD method segregates the {beta}-CoV spike proteins of SARS, SARS-CoV-2, and MERS sequences from other human pathogenic CoV, with clustering consistent with cellular receptor usage. The graphs also suggest evolutionary relationships that may be difficult to determine with conventional bootstrapping methods that require postulating an ancestral sequence. Availability and implementationDGraph is written in Java, compatible with the Java 5 runtime or newer. Source code and executable is available from the GitHub website (https://github.com/bjmnbraun/DGraph/releases). Documentation for installation and use of the software is available from the Readme.md file at (https://github.com/bjmnbraun/DGraph). Contactbjmnbraun@gmail.com or webraun@utmb.edu Supplementary informationSupplementary information Table S1 and Fig. S1 are online available.