Lytras, S. and Hughes, J. (2020) Synonymous dinucleotide usage: a codon-aware metric for quantifying dinucleotide representation in viruses. Viruses, 12(4), 462. (doi: 10.3390/v12040462)
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Abstract
Distinct patterns of dinucleotide representation, such as CpG and UpA suppression, are characteristic of certain viral genomes. Recent research has uncovered vertebrate immune mechanisms that select against specific dinucleotides in targeted viruses. This evidence highlights the importance of systematically examining the dinucleotide composition of viral genomes. We have developed a novel metric, called synonymous dinucleotide usage (SDU), for quantifying dinucleotide representation in coding sequences. Our method compares the abundance of a given dinucleotide to the null hypothesis of equal synonymous codon usage in the sequence. We present a Python3 package, DinuQ, for calculating SDU and other relevant metrics. We have applied this method on two sets of invertebrate- and vertebrate-specific flaviviruses and rhabdoviruses. The SDU shows that the vertebrate viruses exhibit consistently greater under-representation of CpG dinucleotides in all three codon positions in both datasets. In comparison to existing metrics for dinucleotide quantification, the SDU allows for a statistical interpretation of its values by comparing it to a null expectation based on the codon table. Here we apply the method to viruses, but coding sequences of other living organisms can be analysed in the same way.
| Item Type: | Articles |
|---|---|
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Hughes, Dr Joseph and Lytras, Spyros |
| Creator Roles: | Lytras, S.Conceptualization, Methodology, Software, Validation, Formal analysis, Writing – original draft, Visualization Hughes, J.Conceptualization, Formal analysis, Writing – review and editing, Supervision, Project administration |
| Authors: | Lytras, S., and Hughes, J. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
| Journal Name: | Viruses |
| Publisher: | MDPI |
| ISSN: | 1999-4915 |
| ISSN (Online): | 1999-4915 |
| Published Online: | 20 April 2020 |
| Copyright Holders: | Copyright © 2020 The Authors |
| First Published: | First published in Viruses 12(4): 462 |
| Publisher Policy: | Reproduced under a Creative Commons Licence |
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Funder and Project Information
Funder and Project Information