Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond
The appearance of genetic variants impacts vaccination efficiency and therapeutic options, generating a need to map and relate mutations observed in the proteome and the genome. We develop an user-friendly web service software (Viral Instant Mutation Viewer or VIMVer) which allows a direct identific...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-07-01
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| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/15/8/1628 |
| _version_ | 1797583068667576320 |
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| author | Vincent Wilde Bruno Canard François Ferron |
| author_facet | Vincent Wilde Bruno Canard François Ferron |
| author_sort | Vincent Wilde |
| collection | DOAJ |
| description | The appearance of genetic variants impacts vaccination efficiency and therapeutic options, generating a need to map and relate mutations observed in the proteome and the genome. We develop an user-friendly web service software (Viral Instant Mutation Viewer or VIMVer) which allows a direct identification of mutations in the genome and its counterpart in the viral proteome. Since its emergence in 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has generated an overwhelming amount of data while becoming one of the most studied viruses of the Nidovirales order. We originally developed this tool during the COVID pandemic; thus, for any SARS-CoV-2 nucleotide sequence, the web service gives a fast identification, mapping, and display of new mutations simultaneously at the nucleotide and amino acid level in comparison to a reference sequence (Wuhan-1). Furthermore, the lineage or the relative position to the known lineage of the variant of interest is available on the link to Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN COVID-19). The workflow presented here is available online. The source code is released under public license and can be easily adapted for further development to other viruses. |
| first_indexed | 2024-03-10T23:30:42Z |
| format | Article |
| id | doaj.art-6c88d07a20ec4a30bc5e3bb59da795ef |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T23:30:42Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-6c88d07a20ec4a30bc5e3bb59da795ef2023-11-19T03:19:24ZengMDPI AGViruses1999-49152023-07-01158162810.3390/v15081628Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and BeyondVincent Wilde0Bruno Canard1François Ferron2Architecture et Fonction des Macromolécules Biologiques, CNRS-UMR 7257, Polytech Case 925, 13009 Marseille, FranceArchitecture et Fonction des Macromolécules Biologiques, CNRS-UMR 7257, Polytech Case 925, 13009 Marseille, FranceArchitecture et Fonction des Macromolécules Biologiques, CNRS-UMR 7257, Polytech Case 925, 13009 Marseille, FranceThe appearance of genetic variants impacts vaccination efficiency and therapeutic options, generating a need to map and relate mutations observed in the proteome and the genome. We develop an user-friendly web service software (Viral Instant Mutation Viewer or VIMVer) which allows a direct identification of mutations in the genome and its counterpart in the viral proteome. Since its emergence in 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has generated an overwhelming amount of data while becoming one of the most studied viruses of the Nidovirales order. We originally developed this tool during the COVID pandemic; thus, for any SARS-CoV-2 nucleotide sequence, the web service gives a fast identification, mapping, and display of new mutations simultaneously at the nucleotide and amino acid level in comparison to a reference sequence (Wuhan-1). Furthermore, the lineage or the relative position to the known lineage of the variant of interest is available on the link to Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN COVID-19). The workflow presented here is available online. The source code is released under public license and can be easily adapted for further development to other viruses.https://www.mdpi.com/1999-4915/15/8/1628genomicsproteomicsDjangomutationvariantsvirus bioinformatics |
| spellingShingle | Vincent Wilde Bruno Canard François Ferron Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond Viruses genomics proteomics Django mutation variants virus bioinformatics |
| title | Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond |
| title_full | Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond |
| title_fullStr | Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond |
| title_full_unstemmed | Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond |
| title_short | Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond |
| title_sort | viral instant mutation viewer a tool to speed up the identification and analysis of new sars cov 2 emerging variants and beyond |
| topic | genomics proteomics Django mutation variants virus bioinformatics |
| url | https://www.mdpi.com/1999-4915/15/8/1628 |
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