Ribovirus classification by a polymerase barcode sequence

PeerJ

article

Artem Babaian¹  Robert Edgar³ 

[1] St Edmunds College;Department of Haematology, University of Cambridge;Corte Madera

关键词: RNA virus;    RNA-dependent RNA polymerase;    Virus classification;    Virus evolution;   

DOI  :  10.7717/peerj.14055

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

RNA viruses encoding a polymerase gene (riboviruses) dominate the known eukaryotic virome. High-throughput sequencing is revealing a wealth of new riboviruses known only from sequence, precluding classification by traditional taxonomic methods. Sequence classification is often based on polymerase sequences, but standardised methods to support this approach are currently lacking. To address this need, we describe the polymerase palmprint, a segment of the palm sub-domain robustly delineated by well-conserved catalytic motifs. We present an algorithm, Palmscan, which identifies palmprints in nucleotide and amino acid sequences; PALMdb, a collection of palmprints derived from public sequence databases; and palmID, a public website implementing palmprint identification, search, and annotation. Together, these methods demonstrate a proof-of-concept workflow for high-throughput characterisation of RNA viruses, paving the path for the continued rapid growth in RNA virus discovery anticipated in the coming decade.

【 授权许可】

CC BY