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Computational approaches in viral ecology

Dynamic virus-host interactions play a critical role in regulating microbial community structure and function. Yet for decades prior to the genomics era, viruses were largely overlooked in microbial ecology research, as only low-throughput culture-based methods of discovering viruses were available....

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Detalles Bibliográficos
Autores principales: Khot, Varada, Strous, Marc, Hawley, Alyse K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334295/
https://www.ncbi.nlm.nih.gov/pubmed/32670501
http://dx.doi.org/10.1016/j.csbj.2020.06.019
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author Khot, Varada
Strous, Marc
Hawley, Alyse K.
author_facet Khot, Varada
Strous, Marc
Hawley, Alyse K.
author_sort Khot, Varada
collection PubMed
description Dynamic virus-host interactions play a critical role in regulating microbial community structure and function. Yet for decades prior to the genomics era, viruses were largely overlooked in microbial ecology research, as only low-throughput culture-based methods of discovering viruses were available. With the advent of metagenomics, culture-independent techniques have provided exciting opportunities to discover and study new viruses. Here, we review recently developed computational methods for identifying viral sequences, exploring viral diversity in environmental samples, and predicting hosts from metagenomic sequence data. Methods to analyze viruses in silico utilize unconventional approaches to tackle challenges unique to viruses, such as vast diversity, mosaic viral genomes, and the lack of universal marker genes. As the field of viral ecology expands exponentially, computational advances have become increasingly important to gain insight into the role viruses in diverse habitats.
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spelling pubmed-73342952020-07-14 Computational approaches in viral ecology Khot, Varada Strous, Marc Hawley, Alyse K. Comput Struct Biotechnol J Review Article Dynamic virus-host interactions play a critical role in regulating microbial community structure and function. Yet for decades prior to the genomics era, viruses were largely overlooked in microbial ecology research, as only low-throughput culture-based methods of discovering viruses were available. With the advent of metagenomics, culture-independent techniques have provided exciting opportunities to discover and study new viruses. Here, we review recently developed computational methods for identifying viral sequences, exploring viral diversity in environmental samples, and predicting hosts from metagenomic sequence data. Methods to analyze viruses in silico utilize unconventional approaches to tackle challenges unique to viruses, such as vast diversity, mosaic viral genomes, and the lack of universal marker genes. As the field of viral ecology expands exponentially, computational advances have become increasingly important to gain insight into the role viruses in diverse habitats. Research Network of Computational and Structural Biotechnology 2020-06-19 /pmc/articles/PMC7334295/ /pubmed/32670501 http://dx.doi.org/10.1016/j.csbj.2020.06.019 Text en © 2020 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Review Article
Khot, Varada
Strous, Marc
Hawley, Alyse K.
Computational approaches in viral ecology
title Computational approaches in viral ecology
title_full Computational approaches in viral ecology
title_fullStr Computational approaches in viral ecology
title_full_unstemmed Computational approaches in viral ecology
title_short Computational approaches in viral ecology
title_sort computational approaches in viral ecology
topic Review Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334295/
https://www.ncbi.nlm.nih.gov/pubmed/32670501
http://dx.doi.org/10.1016/j.csbj.2020.06.019
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