Ribovirus classification by a polymerase barcode sequence

Abstract

RNA viruses encoding a polymerase gene (riboviruses) dominate the known eukaryotic virome. Next-generation sequencing is revealing a wealth of new riboviruses with uncharacterised phenotypes, precluding classification by traditional taxonomic methods. These are often classified on the basis of polymerase sequence identity, but standardised methods to support this approach are currently lacking. To address this need, we describe the polymerase palmprint, a well-defined segment of the palm sub-domain delineated by well-conserved catalytic motifs. We present a novel algorithm, Palmscan, which identifies palmprints in nucleotide and amino acid sequences. We describe PALMdb, a reference database of palmprints derived from public sequence databases. Palmscan source code and PALMdb data are deposited at https://github.com/rcedgar/palmscan and https://github.com/rcedgar/palmdb, respectively.