key: cord-0827881-0px7p1vx
authors: Krem, Samuel
title: The application of DNA nucleotide footprint plotting in coronavirus
date: 2020-05-21
journal: Inform Med Unlocked
DOI: 10.1016/j.imu.2020.100358
sha: 189bf8c8aa1278f068f1c405e9ebd1ad5623e31d
doc_id: 827881
cord_uid: 0px7p1vx

Direct visualization of the key features of coronavirus genomes can lead to a better understanding of this virus as well as a method to distinguish this type of virus from others. The DNA nucleotide footprint plotter is a tool that makes it possible for straightforward visualization of the characteristics of viral genomes. It can also distinguish different gene types and gene structures. The current project provides a novel tool for biological studies that can contribute to breakthroughs in coronavirus diagnosis, treatment, and prevention.

Coronaviruses are new viruses. Although there have been many timely discoveries for this virus, there are still many things unknown [1, 3] . I designed a novel tool named the DNA nucleotide footprint plotter. corona strains (Fig 6) . Even if the method is designed to observe structural changes at the genomic level that single nucleotide polymorphism calling tools cannot identify, it is possible to show genotype changes and amino acid changes at a single nucleotide resolution. In addition, DNA footprint plotter is a useful tool to determine the evidence of recombination. A recombination between Corona virus There are three ways to plot DNA footprint plots. They are ACat, AGac, and ATag. ACat is used as an example. If the nucleotide is A, then x value plusses 1 (X+1). If the nucleotide is T, then x value minuses 1 (X-1). If the nucleotide is C, then y value plusses 1 (Y+1). If the nucleotide is G, then y value minuses 1 (Y- The method aims to demonstrate structural variations at higher levels that single nucleotide mutation callers cannot identify. However, the tool can precisely demonstrate single nucleotide information (Fig6). The method itself has no limit to plot the number of nucleotide bases. But due to the size of computer screens and paper, too many bases will cause the lines to overlay each other. Thus the sizes of virus genome or segments of eukaryote genome are recommended for one particular plot. One plot can display a complete virus genome, and users can combine multiple plots together to visualize more complicated genomes such as the genomes of eukaryotes. Or if only a partial virus genome or a particular gene are of interest, the corresponding regions can be displayed by DNA foot plotter. 

Coronavirus demonstrates a unique footprint (Fig 1) , and so do other types of viruses (Fig 2-5 13 DNA footprint plotter is useful for character identification at the genome level. It can identify key features in the genome that single nucleotide mutation callers will miss. It can also be used as an add-on tool of phylogenic trees. Phylogenic trees are very useful to group and compare viruses. But the detailed differences are not shown. If we can also apply DNA footprint plot, people will have a better idea regarding which regions are similar and which regions are different, as well as the patterns of differences.

In addition to viruses, DNA footprint plots can be applied to visualize single genes or groups of genes in higher organisms to facilitate the understanding of gene structure. It can also help to identify diseasecausing structural variations such as repeats in diseases like Huntington's disease.

If we digitalize the key features of the footprint shapes within genomes and genes, we can use machine learning, such as neural networks, to recognize various viruses and genes [5] .

DNA footprint plotter is a novel tool to display the characteristics of virus genome, genes, and sections of eukaryote genome. It is a quick and convenient method to visualized the features of corona virus DNA to distinguish them from other viruses, and to understand the differences of coronavirus sub species.

A new coronavirus associated with human respiratory disease in China

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

COVID-19: Knowns, Unknowns, and Questions. mSphere

Virus Variation Resource-improved response to emergent viral outbreaks

Deep learning for biology

pdf I do not have any financial or personal relationships with other people or organizations that could inappropriately influence (bias) my work. I do not have potential competing interests include employment, consultancies, stock ownership, honoraria, paid expert testimony

I want to thank my school Buckingham Browne & Nichols for teaching me essential knowledge in biology and Java programming skills to make this paper possible. I also want to thank my family to excuse me from house chores and to give me time to work on the project.