Phage hunters: Computational strategies for finding phages in large-scale 'omics datasets

Virus Research
Bonnie L HurwitzJana M U'Ren

Abstract

A plethora of tools exist for identifying phage sequences in bacterial genomes, single cell amplified genomes, and host-associated and environmental metagenomes. Yet because the genetics of phages and their hosts are closely intertwined, distinguishing viral from bacterial signal remains an ongoing challenge. Further the size, quantity and fragmentary nature of modern 'omics datasets ushers in a new set of computational challenges. Here, we detail the promises and pitfalls of using currently available gene-centric or k-mer based tools for identifying prophage sequences in genomes and prophage and viral contigs in metagenomes. Each of these methods offers a unique piece of the puzzle to elucidating the intriguing signatures of phage-host coevolution.

References

Mar 8, 2000·Microbiology and Molecular Biology Reviews : MMBR·K E Wommack, R R Colwell
Jul 31, 2003·Molecular Microbiology·Sherwood Casjens
Aug 15, 2003·Nature·Nicholas H MannMartha Clokie
Nov 1, 1952·Journal of Bacteriology·N D ZINDER, J LEDERBERG
Jul 17, 2004·Proceedings of the National Academy of Sciences of the United States of America·Debbie LindellSallie W Chisholm
Jul 21, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew MillardNicholas H Mann
Apr 15, 2005·PLoS Biology·Matthew B SullivanSallie W Chisholm
Jun 7, 2005·Trends in Microbiology·Mya Breitbart, Forest Rohwer
Nov 17, 2006·Environmental Microbiology·Martha R J Clokie, Nicholas H Mann
Sep 1, 1956·Genetics·M L MorseJ Lederberg
Jun 15, 2007·Environmental Microbiology·Peter R WeigeleRoger W Hendrix
Feb 2, 2008·Bioinformatics·Gipsi Lima-MendezRaphaël Leplae
Mar 22, 2008·Current Biology : CB·Thorben DammeyerNicole Frankenberg-Dinkel
Mar 21, 2009·Nature Protocols·Rebecca V ThurberForest Rohwer
Aug 17, 2010·Bioinformatics·Robert C Edgar
Sep 2, 2010·Nucleic Acids Research·Mina RhoYuzhen Ye
Oct 12, 2010·Science·Lauren D McDanielJohn H Paul
Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Itai SharonTomer Shlomi
Jun 16, 2011·Nucleic Acids Research·You ZhouDavid S Wishart
Aug 17, 2011·Proceedings of the National Academy of Sciences of the United States of America·Luke R ThompsonSallie W Chisholm
May 12, 2012·BMC Bioinformatics·Adam L Bazinet, Michael P Cummings
Jun 12, 2012·Nature Reviews. Microbiology·Andrew S LangJ Thomas Beatty
Feb 15, 2013·The ISME Journal·Jeremy A FrankAlex B Burgin
Feb 15, 2013·Standards in Genomic Sciences·K Eric WommackDaniel J Nasko
Mar 4, 2014·Genome Biology·Derrick E Wood, Steven L Salzberg
Jul 9, 2014·Proceedings of the National Academy of Sciences of the United States of America·Bonnie L HurwitzMatthew B Sullivan
Nov 18, 2014·Nature Methods·Benjamin BuchfinkDaniel H Huson
May 23, 2015·Science·Jennifer R BrumMatthew B Sullivan
Jun 4, 2015·PeerJ·Simon RouxMatthew B Sullivan
Jul 29, 2015·BMC Genomics·Tasha M Santiago-RodriguezDavid T Pride
Aug 22, 2015·The ISME Journal·Jennifer R BrumMatthew B Sullivan
Sep 10, 2015·Proceedings of the National Academy of Sciences of the United States of America·Alejandro ReyesJeffrey I Gordon
Dec 15, 2015·FEMS Microbiology Reviews·Robert A EdwardsBas E Dutilh

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Citations

Jan 1, 2019·GigaScience·Illyoung ChoiBonnie L Hurwitz
May 7, 2019·Frontiers in Microbiology·Alise J Ponsero, Bonnie L Hurwitz
Jul 28, 2020·Genes·Christine CittiLaurent-Xavier Nouvel
Aug 23, 2018·Frontiers in Genetics·Deyvid AmgartenJoão C Setubal
Feb 3, 2019·Biochemical Society Transactions·Kira S MakarovaEugene V Koonin
Oct 15, 2020·Viruses·Rasmus Riemer JakobsenDennis Sandris Nielsen

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