Please use this identifier to cite or link to this item: https://doi.org/10.1371/journal.pcbi.1007345
Title: A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance
Authors: Skittrall, J.P.
Ingemarsdotter, C.K.
Gog, J.R.
Lever, A.M.L. 
Issue Date: 2019
Publisher: Public Library of Science
Citation: Skittrall, J.P., Ingemarsdotter, C.K., Gog, J.R., Lever, A.M.L. (2019). A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance. PLoS Computational Biology 15 (9) : e1007345. ScholarBank@NUS Repository. https://doi.org/10.1371/journal.pcbi.1007345
Rights: Attribution 4.0 International
Abstract: HIV-1 replicates via a low-fidelity polymerase with a high mutation rate; strong conservation of individual nucleotides is highly indicative of the presence of critical structural or functional properties. Identifying such conservation can reveal novel insights into viral behaviour. We analysed 3651 publicly available sequences for the presence of nucleic acid conservation beyond that required by amino acid constraints, using a novel scale-free method that identifies regions of outlying score together with a codon scoring algorithm. Sequences with outlying score were further analysed using an algorithm for producing local RNA folds whilst accounting for alignment properties. 11 different conserved regions were identified, some corresponding to well-known cis-acting functions of the HIV-1 genome but also others whose conservation has not previously been noted. We identify rational causes for many of these, including cis functions, possible additional reading frame usage, a plausible mechanism by which the central polypurine tract primes second-strand DNA synthesis and a conformational stabilising function of a region at the 50 end of env. © 2019 Skittrall et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Source Title: PLoS Computational Biology
URI: https://scholarbank.nus.edu.sg/handle/10635/213744
ISSN: 1553734X
DOI: 10.1371/journal.pcbi.1007345
Rights: Attribution 4.0 International
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This item is licensed under a Creative Commons License Creative Commons