Computational approaches in viral ecology

Computational and Structural Biotechnology Journal
Varada KhotAlyse K Hawley

Abstract

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.

References

Jun 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·C R WoeseM L Wheelis
Sep 1, 1971·Bacteriological Reviews·D Baltimore
Aug 4, 1998·Applied and Environmental Microbiology·S C Jiang, J H Paul
Dec 10, 1998·Nucleic Acids Research·H OgataM Kanehisa
Jul 27, 2002·Journal of Bacteriology·Forest Rohwer, Rob Edwards
Apr 12, 2003·The New England Journal of Medicine·Christian DrostenHans Wilhelm Doerr
May 29, 2004·Bioinformatics·Stefan R HenzStephan C Schuster
Dec 14, 2007·Genome Research·Victor KuninPhilip Hugenholtz
Feb 1, 2008·Molecular Biology and Evolution·Gipsi Lima-MendezRaphaël Leplae
Feb 2, 2008·Bioinformatics·Gipsi Lima-MendezRaphaël Leplae
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Jan 9, 2010·Science·Philippe Horvath, Rodolphe Barrangou
Oct 16, 2010·Nucleic Acids Research·Chantal HuloPhilippe Le Mercier
Jan 11, 2011·Bioinformatics·Guillaume Marçais, Carl Kingsford
Mar 24, 2012·Current Opinion in Virology·John L MokiliBas E Dutilh
Oct 23, 2012·Virology·Melissa B Duhaime, Matthew B Sullivan
Nov 30, 2012·Nucleic Acids Research·Dennis A BensonEric W Sayers
Dec 19, 2013·PLoS Genetics·Carolina Megumi MizunoRohit Ghai
Mar 13, 2014·FEMS Microbiology Reviews·Britt Koskella, Michael A Brockhurst
Apr 9, 2014·Proceedings of the National Academy of Sciences of the United States of America·Peter C FineranStan J J Brouns
May 20, 2014·Applied and Environmental Microbiology·Evelien M Adriaenssens, Don A Cowan
Nov 28, 2014·Nucleic Acids Research·J Rodney BristerOlga Blinkova
Jun 4, 2015·PeerJ·Simon RouxMatthew B Sullivan
Oct 7, 2015·Frontiers in Microbiology·Lesley A Ogilvie, Brian V Jones
Dec 15, 2015·FEMS Microbiology Reviews·Robert A EdwardsBas E Dutilh
Jan 18, 2016·Trends in Microbiology·Eduardo CorelEric Bapteste
Mar 5, 2016·Viruses·Tomoko MiharaHiroyuki Ogata
May 5, 2016·Nucleic Acids Research·David ArndtDavid S Wishart
May 7, 2016·Viruses·Julia VillarroelMette Voldby Larsen
Jul 15, 2016·Microbiology and Molecular Biology Reviews : MMBR·Stineke van HouteEdze R Westra
Aug 18, 2016·Nature·David Paez-EspinoNikos C Kyrpides
Oct 30, 2016·Nucleic Acids Research·Ana Laura GrazziotinDavid M Kristensen
Apr 6, 2017·Bioinformatics·Yosuke NishimuraSusumu Goto
Apr 30, 2017·Communicative & Integrative Biology·Jaime IranzoEugene V Koonin
Jul 6, 2017·Nature Communications·Felipe H CoutinhoFabiano L Thompson
Jul 28, 2017·Nature Protocols·David Paez-EspinoNikos C Kyrpides
Aug 23, 2017·World Journal of Gastrointestinal Pharmacology and Therapeutics·Derek M LinHenry C Lin

❮ Previous
Next ❯

Methods Mentioned

BETA
electron microscopy

Software Mentioned

IMG
UVAB
BLASTn
Phage
Prophinder
VirSorter
VIBRANT
Phaster
Crass
Host Taxon Predictor

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Current Opinion in Virology
Karyna Rosario, Mya Breitbart
Indian Journal of Virology : an Official Organ of Indian Virological Society
S V Alavandi, M Poornima
Nature
David Paez-EspinoNikos C Kyrpides
© 2021 Meta ULC. All rights reserved