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Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs S, Hattab G, Hauschild AC, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O’Toole ÁN, Ontiveros-Palacios N, Petrov AI, Rangel-Pineros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Brief Bioinform 2021; 22:642-663. [PMID: 33147627 PMCID: PMC7665365 DOI: 10.1093/bib/bbaa232] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/28/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Christian Brandt
- Institute of Infectious Disease and Infection Control at Jena University Hospital, Germany
| | - Marco Cacciabue
- Consejo Nacional de Investigaciones Científicas y Tócnicas (CONICET) working on FMDV virology at the Instituto de Agrobiotecnología y Biología Molecular (IABiMo, INTA-CONICET) and at the Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Argentina
| | | | - Oliver Drechsel
- bioinformatics department at the Robert Koch-Institute, Germany
| | | | - Adrian Fritz
- Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research, Germany
| | - Stephan Fuchs
- bioinformatics department at the Robert Koch-Institute, Germany
| | - Georges Hattab
- Bioinformatics Division at Philipps-University Marburg, Germany
| | | | - Dominik Heider
- Data Science in Biomedicine at the Philipps-University of Marburg, Germany
| | | | | | - Stefan Hoops
- Biocomplexity Institute and Initiative at the University of Virginia, USA
| | - Lars Kaderali
- Bioinformatics and head of the Institute of Bioinformatics at University Medicine Greifswald, Germany
| | | | - Max von Kleist
- bioinformatics department at the Robert Koch-Institute, Germany
| | - Renó Kmiecinski
- bioinformatics department at the Robert Koch-Institute, Germany
| | | | - Gorka Lasso
- Chandran Lab, Albert Einstein College of Medicine, USA
| | | | | | | | | | | | | | - Alice C McHardy
- Computational Biology of Infection Research Lab at the Helmholtz Centre for Infection Research in Braunschweig, Germany
| | - Pedro Mendes
- Center for Quantitative Medicine of the University of Connecticut School of Medicine, USA
| | | | - Vincent Navratil
- Bioinformatics and Systems Biology at the Rhône Alpes Bioinformatics core facility, Universitó de Lyon, France
| | | | | | | | | | | | - Nicole Redaschi
- Development of the Swiss-Prot group at the SIB for UniProt and SIB resources that cover viral biology (ViralZone)
| | - Susanne Reimering
- Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research
| | | | | | | | | | - Sepideh Sadegh
- Chair of Experimental Bioinformatics at Technical University of Munich, Germany
| | - Joshua B Singer
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | | | - Chris Upton
- Department of Biochemistry and Microbiology, University of Victoria, Canada
| | | | | | - Manja Marz
- Friedrich Schiller University Jena, Germany
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Kalvari I, Nawrocki EP, Ontiveros-Palacios N, Argasinska J, Lamkiewicz K, Marz M, Griffiths-Jones S, Toffano-Nioche C, Gautheret D, Weinberg Z, Rivas E, Eddy SR, Finn RD, Bateman A, Petrov AI. Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res 2021; 49:D192-D200. [PMID: 33211869 PMCID: PMC7779021 DOI: 10.1093/nar/gkaa1047] [Citation(s) in RCA: 336] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022] Open
Abstract
Rfam is a database of RNA families where each of the 3444 families is represented by a multiple sequence alignment of known RNA sequences and a covariance model that can be used to search for additional members of the family. Recent developments have involved expert collaborations to improve the quality and coverage of Rfam data, focusing on microRNAs, viral and bacterial RNAs. We have completed the first phase of synchronising microRNA families in Rfam and miRBase, creating 356 new Rfam families and updating 40. We established a procedure for comprehensive annotation of viral RNA families starting with Flavivirus and Coronaviridae RNAs. We have also increased the coverage of bacterial and metagenome-based RNA families from the ZWD database. These developments have enabled a significant growth of the database, with the addition of 759 new families in Rfam 14. To facilitate further community contribution to Rfam, expert users are now able to build and submit new families using the newly developed Rfam Cloud family curation system. New Rfam website features include a new sequence similarity search powered by RNAcentral, as well as search and visualisation of families with pseudoknots. Rfam is freely available at https://rfam.org.
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Affiliation(s)
- Ioanna Kalvari
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Nancy Ontiveros-Palacios
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joanna Argasinska
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Sam Griffiths-Jones
- Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Claire Toffano-Nioche
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Daniel Gautheret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, 04107 Leipzig, Germany
| | - Elena Rivas
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sean R Eddy
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.,John A. Paulson School of Engineering and Applied Science, Harvard University, Cambridge, MA 02138, USA
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anton I Petrov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Abstract
Riboswitches are genetic control elements located mainly within the 5' untranslated regions of messenger RNAs. These RNA elements undergo conformational changes that modulate gene expression upon binding of regulatory signals including vitamins, amino acids, nucleobases and uncharged tRNA. The thiamin pyrophosphate (TPP)-binding riboswitch (THI-box) is found in all three kingdoms of life and can regulate gene expression at the levels of premature termination of transcription, initiation of translation and mRNA splicing. The THI-box is composed of two parallel stacked helices bound by another helix in a three-way junction. We performed an in vivo expression analysis of mutants with substitutions in conserved bases located at the interior and terminal loops of the Escherichia coli thiM THI-box, which is translationally regulated, and observed two different phenotypic classes. One class exhibited high expression during growth in the presence or absence of thiamin, while the second class exhibited low expression regardless of the presence of thiamin. Accessibility of the Shine-Dalgarno region of the RNA following the addition of TPP was monitored by means of an oligonucleotide-dependent RNase H cleavage assay, and binding of 30S ribosomal subunits. These studies showed that high- and low-expression mutant RNAs are locked in the non-repressive and repressive conformations respectively.
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Affiliation(s)
- Nancy Ontiveros-Palacios
- Depto. de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos 62250, México
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Abstract
We present a computational approach that identifies regulatory elements conserved across phylogenetically distant organisms. Intergenic regulatory regions were clustered by orthology of the adjacent genes, and an iterative process was applied to search for significant motifs, enabling new elements of the putative regulon to be added in each cycle. With this approach, we identified highly conserved riboswitches and the Gram positive T-box. Interestingly, we identified many other regulatory systems that appear to depend on conserved RNA structures.
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Affiliation(s)
- Cei Abreu-Goodger
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, 62210 Morelos, México
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