VirusViz: comparative analysis and effective visualization of viral nucleotide and amino acid variants.

Nucleic Acids Research
Anna BernasconiStefano Ceri

Abstract

Variant visualization plays an important role in supporting the viral evolution analysis, extremely valuable during the COVID-19 pandemic. VirusViz is a web-based application for comparing variants of selected viral populations and their sub-populations; it is primarily focused on SARS-CoV-2 variants, although the tool also supports other viral species (SARS-CoV, MERS-CoV, Dengue, Ebola). As input, VirusViz imports results of queries extracting variants and metadata from the large database ViruSurf, which integrates information about most SARS-CoV-2 sequences publicly deposited worldwide. Moreover, VirusViz accepts sequences of new viral populations as multi-FASTA files plus corresponding metadata in CSV format; a bioinformatic pipeline builds a suitable input for VirusViz by extracting the nucleotide and amino acid variants. Pages of VirusViz provide metadata summarization, variant descriptions, and variant visualization with rich options for zooming, highlighting variants or regions of interest, and switching from nucleotides to amino acids; sequences can be grouped, groups can be comparatively analyzed. For SARS-CoV-2, we manually collect mutations with known or predicted levels of severity/virulence, as indicated in linked ...Continue Reading

References

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Dec 11, 2019·Database : the Journal of Biological Databases and Curation·Arif CanakogluStefano Ceri
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Oct 13, 2020·Nucleic Acids Research·Arif CanakogluStefano Ceri
Oct 13, 2020·Nucleic Acids Research·Shuyi FangJun Wan
Nov 19, 2020·Journal of Medical Virology·Daniele MercatelliFederico M Giorgi
Dec 22, 2020·Briefings in Bioinformatics·Anna BernasconiStefano Ceri
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Feb 12, 2021·JAMA : the Journal of the American Medical Association·Wenjuan ZhangEric Vail
Feb 12, 2021·The Lancet Infectious Diseases·Intikhab AlamTakashi Gojobori

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