2021
DOI: doi.org/10.7490/f1000research.1118746.1
Published: F1000Research Bioinformatics Education and Training Collection
Abstract
This Practical Guide outlines basic bioinformatics approaches for exploring the SARS-CoV-2 genome and its corresponding proteins, focusing on the protein exposed on the viral particle surface: the spike protein. The ways in which bioinformatics can be harnessed to study a new virus, its genome, its proteins, its origins and its evolution are explored.
Specifically, this Guide introduces a range of bioinformatics tools for comparing and analysing nucleotide and protein sequences. On reading the Guide and completing the exercises, you will be able to:
– discover SARS-CoV-2 genome(s) available in a public nucleotide repository;
– compare SARS-CoV-2 genome sequences, look for their differences (mutations) and identify the variants;
– translate the spike gene into its encoded protein sequence;
– discover the 3D structure of the spike protein;
– understand the impact of mutations on infectivity and immune responses; and
– infer the origin of SARS-CoV-2 by comparing coronavirus spike protein sequences from different animal origins.