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Ribovirus classification by a polymerase barcode sequence

View ORCID ProfileArtem Babaian, View ORCID ProfileRobert C. Edgar
doi: https://doi.org/10.1101/2021.03.02.433648
Artem Babaian
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Robert C. Edgar
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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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/rcedgar/palmdb

  • https://github.com/rcedgar/palmscan

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 03, 2021.
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Ribovirus classification by a polymerase barcode sequence
Artem Babaian, Robert C. Edgar
bioRxiv 2021.03.02.433648; doi: https://doi.org/10.1101/2021.03.02.433648
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Ribovirus classification by a polymerase barcode sequence
Artem Babaian, Robert C. Edgar
bioRxiv 2021.03.02.433648; doi: https://doi.org/10.1101/2021.03.02.433648

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