UNIQmin, an alignment-free tool to study viral sequence diversity across taxonomic lineages: a case study of monkeypox virus

Sequence changes in viral genomes generate protein sequence diversity that enable viruses to evade the host immune system, hindering the development of effective preventive and therapeutic interventions. Massive proliferation of sequence data provides unprecedented opportunities to study viral adaptation and evolution. Alignment-free approach removes various restrictions, otherwise posed by an alignment-dependent approach for the study of sequence diversity. The publicly available tool, UNIQmin offers an alignment-free approach for the study of viral sequence diversity at any given rank of taxonomy lineage and is big data ready. The tool performs an exhaustive search to determine the minimal set of sequences required to capture the peptidome diversity within a given dataset. This compression is possible through the removal of identical sequences and unique sequences that do not contribute effectively to the peptidome diversity pool. Herein, we describe a detailed three-part protocol utilizing UNIQmin to generate the minimal set for the purpose of viral diversity analyses, alignment-free at any rank of the taxonomy lineage, using the latest global public health threat monkeypox virus (MPX) as a case study. This protocol enables systematic diversity study across the taxonomic lineage, which are much needed for our future preparedness of a viral epidemic, in particular when data is in abundance, freely available, and alignment is not an option.