2021
DOI: 10.3390/math9172063
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A Mathematical Analysis of HDV Genotypes: From Molecules to Cells

Abstract: Hepatitis D virus (HDV) is classified according to eight genotypes. The various genotypes are included in the HDVdb database, where each HDV sequence is specified by its genotype. In this contribution, a mathematical analysis is performed on RNA sequences in HDVdb. The RNA folding predicted structures of the Genbank HDV genome sequences in HDVdb are classified according to their coarse-grain tree-graph representation. The analysis allows discarding in a simple and efficient way the vast majority of the sequenc… Show more

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Cited by 5 publications
(8 citation statements)
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“…A zoom-in of Figure 3(A) in [4], where the folding prediction by energy minimization using either mfold/UNAFold [8] or Vienna's RNAfold [9] of MG711735 from genotype 7 [5] is performed, with an SL1-like hairpin that contains the sub-sequence "GAAC" as in SL1 from genotype 3. The secondary structure is drawn using VARNA [10].…”
Section: Figurementioning
confidence: 99%
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“…A zoom-in of Figure 3(A) in [4], where the folding prediction by energy minimization using either mfold/UNAFold [8] or Vienna's RNAfold [9] of MG711735 from genotype 7 [5] is performed, with an SL1-like hairpin that contains the sub-sequence "GAAC" as in SL1 from genotype 3. The secondary structure is drawn using VARNA [10].…”
Section: Figurementioning
confidence: 99%
“…It starts with a mathematical analysis of the RNA motifs in viruses, analyzing data from the web resource RNASIV (RNA structure in viruses) [2] in order to categorize the various RNA structures based on their tree-graph properties via an eigenvalue analysis [3], with the second eigenvalue of the Laplacian matrix belonging to the coarse-grained tree-graph of the RNA secondary structure being examined. The same concept is carried out in [4] for an eigenvalue analysis of HDVdb [5], a database of HDV sequences that is divided into various HDV genotypes, in order to predict whether the peculiar RNA-editing mechanism achieved by a conformational switch in RNA that is known to occur in HDV genotype 3 [6] can occur in other genotypes as well. Two publications that appeared independently at around the same time [4,7] addressed this problem.…”
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confidence: 99%
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“…Pearson's correlation test has been performed, p = 0.37, r = 0.17. fully characterizing quasispecies involving congruent mutations, for example, linked to secondary structure on a unique variant molecule would be of interest. Indeed, as highlighted by Zack et al, the availability of full-length sequences is mandatory for RNA structural analyses and structure/function studies 50. Additionally, knowledge of the evolution of circulating complete genomes during the natural history of HDV infection and under treatment are currently missing.…”
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confidence: 99%