VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
Background Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Results Here...
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| Vydáno v: | Microbiome Ročník 9; číslo 1; s. 37 - 13 |
|---|---|
| Hlavní autoři: | , , , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
London
BioMed Central
01.02.2021
Springer Nature B.V BMC |
| Témata: | |
| ISSN: | 2049-2618, 2049-2618 |
| On-line přístup: | Získat plný text |
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| Abstract | Background
Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools.
Results
Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order
Caudovirales
). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity.
Conclusion
With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available (
https://bitbucket.org/MAVERICLab/virsorter2
), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse (
https://de.cyverse.org/de
).
1yUdaVB8pb7ryNSffJakk6
Video abstract |
|---|---|
| AbstractList | Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available (https://bitbucket.org/MAVERICLab/virsorter2), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse (https://de.cyverse.org/de). Abstract Background Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Results Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. Conclusion With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse ( https://de.cyverse.org/de ). Video abstract Viruses are a significant player in many biosphere and human ecosystems, but most signals remain "hidden" in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools.BACKGROUNDViruses are a significant player in many biosphere and human ecosystems, but most signals remain "hidden" in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools.Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2's modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity.RESULTSHere, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2's modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity.With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse ( https://de.cyverse.org/de ). Video abstract.CONCLUSIONWith multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse ( https://de.cyverse.org/de ). Video abstract. Background Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Results Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. Conclusion With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available (https://bitbucket.org/MAVERICLab/virsorter2), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse (https://de.cyverse.org/de). Video abstract Background : Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Results : Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. Conclusion : With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available (https://bitbucket.org/MAVERICLab/virsorter2), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse (https://de.cyverse.org/de). Viruses are a significant player in many biosphere and human ecosystems, but most signals remain "hidden" in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2's modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse ( https://de.cyverse.org/de ). Video abstract. Background Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Results Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales ). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. Conclusion With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse ( https://de.cyverse.org/de ). 1yUdaVB8pb7ryNSffJakk6 Video abstract |
| ArticleNumber | 37 |
| Author | Sullivan, Matthew B. Guo, Jiarong Bolduc, Ben Dominguez-Huerta, Guillermo Vik, Dean Delmont, Tom O. Pratama, Akbar Adjie Zayed, Ahmed A. Gazitúa, M. Consuelo Varsani, Arvind Roux, Simon |
| Author_xml | – sequence: 1 givenname: Jiarong surname: Guo fullname: Guo, Jiarong organization: Department of Microbiology, Ohio State University – sequence: 2 givenname: Ben surname: Bolduc fullname: Bolduc, Ben organization: Department of Microbiology, Ohio State University – sequence: 3 givenname: Ahmed A. surname: Zayed fullname: Zayed, Ahmed A. organization: Department of Microbiology, Ohio State University – sequence: 4 givenname: Arvind surname: Varsani fullname: Varsani, Arvind organization: The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town – sequence: 5 givenname: Guillermo surname: Dominguez-Huerta fullname: Dominguez-Huerta, Guillermo organization: Department of Microbiology, Ohio State University – sequence: 6 givenname: Tom O. surname: Delmont fullname: Delmont, Tom O. organization: Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay – sequence: 7 givenname: Akbar Adjie surname: Pratama fullname: Pratama, Akbar Adjie organization: Department of Microbiology, Ohio State University – sequence: 8 givenname: M. Consuelo surname: Gazitúa fullname: Gazitúa, M. Consuelo organization: Viromica – sequence: 9 givenname: Dean surname: Vik fullname: Vik, Dean organization: Department of Microbiology, Ohio State University – sequence: 10 givenname: Matthew B. orcidid: 0000-0001-8398-8234 surname: Sullivan fullname: Sullivan, Matthew B. email: sullivan.948@osu.edu organization: Department of Microbiology, Ohio State University, Civil, Environmental and Geodetic Engineering, Ohio State University, Center of Microbiome Science, Ohio State University – sequence: 11 givenname: Simon surname: Roux fullname: Roux, Simon email: sroux@lbl.gov organization: DOE Joint Genome Institute, Lawrence Berkeley National Laboratory |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33522966$$D View this record in MEDLINE/PubMed https://cea.hal.science/cea-04284766$$DView record in HAL https://www.osti.gov/biblio/1763830$$D View this record in Osti.gov |
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| Cites_doi | 10.7554/eLife.51971.sa2 10.1186/s12859-019-3019-7 10.3389/fgene.2018.00304 10.1093/bioinformatics/bts480 10.1101/2020.05.06.081778 10.1038/nbt.3935 10.1038/s41564-018-0190-y 10.1186/s40168-019-0768-5 10.3389/fmicb.2019.00806 10.1038/s41587-019-0100-8 10.1038/nrmicro1163 10.1038/s41564-018-0166-y 10.1042/BST0390036 10.1038/nrmicro2853 10.1101/855387 10.1093/nar/gkr485 10.1186/1471-2148-9-112 10.1038/nature19094 10.1038/nature19366 10.1186/s40168-017-0283-5 10.1128/mSystems.00120-19 10.1093/nar/gkl732 10.1002/bies.201200083 10.1038/nmeth.1938 10.1038/nrmicro.2017.87 10.1093/nar/gkw387 10.1002/bies.201200174 10.1038/s41586-018-0012-7 10.1093/nar/gky995 10.1111/j.1574-6976.1996.tb00239.x 10.1371/journal.pcbi.1002195 10.1101/836445 10.1128/JVI.03289-14 10.1186/1471-2105-11-119 10.1038/s41467-020-15507-2 10.1128/MMBR.00061-19 10.1093/nar/gkv1189 10.1093/bioinformatics/btn043 10.1046/j.1365-2958.2003.03580.x 10.1126/science.1153213 10.1128/JB.00052-20 10.1016/j.cell.2019.03.040 10.1093/nar/gkx932 10.1038/s41579-019-0191-8 10.1038/s41564-019-0510-x 10.1038/nbt.4306 10.1128/MRA.01325-18 10.7554/eLife.05378 10.1038/nrmicro3404 10.1093/nar/gkh340 10.1126/science.1261498 10.7717/peerj.3428 10.7717/peerj.985 10.1007/s40484-019-0187-4 10.1073/pnas.96.5.2192 10.1093/nar/gks406 10.1016/j.cell.2017.10.045 10.1038/s41592-018-0046-7 10.1093/nar/gky1127 10.1038/nature20167 10.1038/nbt.3988 10.1038/nbt.3893 10.1038/nrmicro.2016.83 10.1126/sciadv.aay5981 10.7554/eLife.08490 10.1038/s41586-020-1957-x 10.1128/JVI.00582-20 10.1038/s41467-017-01086-2 |
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| References | M Krupovic (990_CR55) 2009; 9 RC Edgar (990_CR65) 2004; 32 M Breitbart (990_CR20) 2018; 3 M Krupovic (990_CR54) 2012; 34 N Fierer (990_CR2) 2017; 15 D Hyatt (990_CR41) 2010; 11 990_CR59 RM Bowers (990_CR6) 2017; 35 990_CR23 SR Eddy (990_CR66) 2009; 23 990_CR67 990_CR22 J Callanan (990_CR45) 2020; 6 J Wang (990_CR4) 2016; 14 W Zillig (990_CR56) 1996; 18 B Grüning (990_CR71) 2018; 15 AC Gregory (990_CR16) 2019; 177 M Moniruzzaman (990_CR26) 2020; 11 J Ren (990_CR33) 2017; 5 H Bin Jang (990_CR62) 2019; 37 M Shi (990_CR24) 2016; 540 RW Hendrix (990_CR13) 1999; 96 D Arndt (990_CR30) 2016; 44 D Paez-Espino (990_CR47) 2019; 7 M Steinegger (990_CR61) 2019; 20 A Reyes (990_CR7) 2012; 10 S El-Gebali (990_CR43) 2019; 47 990_CR53 SR Eddy (990_CR42) 2011; 7 DE Fouts (990_CR69) 2006; 34 AR Mushegian (990_CR14) 2020; 202 D Paez-Espino (990_CR17) 2016; 536 D Paez-Espino (990_CR18) 2019; 47 DR Vik (990_CR38) 2017; 5 JR Brum (990_CR12) 2015; 348 Y Zhou (990_CR68) 2011; 39 S Roux (990_CR9) 2019; 37 M Shi (990_CR25) 2018; 556 990_CR37 990_CR39 S Roux (990_CR48) 2015; 4 F Schulz (990_CR19) 2020; 578 G Ofir (990_CR21) 2018; 172 C Quince (990_CR5) 2017; 35 EJ Lefkowitz (990_CR52) 2018; 46 990_CR40 M Steinegger (990_CR60) 2017; 35 JR Brum (990_CR36) 2015; 13 990_CR44 S Casjens (990_CR51) 2003; 49 T Nepusz (990_CR64) 2012; 9 J Ren (990_CR34) 2020; 8 ED Sonnenburg (990_CR3) 2019; 17 S Roux (990_CR46) 2017; 8 RA Edwards (990_CR10) 2005; 3 PG Falkowski (990_CR1) 2008; 320 S Roux (990_CR29) 2015; 3 F Pedregosa (990_CR50) 2011; 12 G Lima-Mendez (990_CR27) 2008; 24 S Roux (990_CR35) 2019; 4 N Soler (990_CR57) 2011; 39 JB Emerson (990_CR63) 2018; 3 S Akhter (990_CR28) 2012; 40 MB Sullivan (990_CR11) 2015; 89 990_CR32 990_CR31 D Willner (990_CR8) 2013; 35 NA O’Leary (990_CR49) 2016; 44 J Köster (990_CR58) 2012; 28 S Roux (990_CR15) 2016; 537 990_CR70 |
| References_xml | – ident: 990_CR22 doi: 10.7554/eLife.51971.sa2 – volume: 20 start-page: 473 year: 2019 ident: 990_CR61 publication-title: BMC Bioinformatics doi: 10.1186/s12859-019-3019-7 – ident: 990_CR31 doi: 10.3389/fgene.2018.00304 – volume: 28 start-page: 2520 year: 2012 ident: 990_CR58 publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts480 – ident: 990_CR59 doi: 10.1101/2020.05.06.081778 – volume: 35 start-page: 833 year: 2017 ident: 990_CR5 publication-title: Nat Biotechnol doi: 10.1038/nbt.3935 – volume: 3 start-page: 870 year: 2018 ident: 990_CR63 publication-title: Nat Microbiol doi: 10.1038/s41564-018-0190-y – volume: 7 start-page: 157 year: 2019 ident: 990_CR47 publication-title: Microbiome doi: 10.1186/s40168-019-0768-5 – ident: 990_CR39 doi: 10.3389/fmicb.2019.00806 – volume: 37 start-page: 632 year: 2019 ident: 990_CR62 publication-title: Nat Biotechnol doi: 10.1038/s41587-019-0100-8 – volume: 3 start-page: 504 year: 2005 ident: 990_CR10 publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro1163 – volume: 3 start-page: 754 year: 2018 ident: 990_CR20 publication-title: Nat Microbiol doi: 10.1038/s41564-018-0166-y – volume: 39 start-page: 36 year: 2011 ident: 990_CR57 publication-title: Biochem Soc Trans doi: 10.1042/BST0390036 – volume: 10 start-page: 607 year: 2012 ident: 990_CR7 publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro2853 – ident: 990_CR32 doi: 10.1101/855387 – volume: 39 start-page: W347 year: 2011 ident: 990_CR68 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkr485 – volume: 9 start-page: 112 year: 2009 ident: 990_CR55 publication-title: BMC Evol Biol doi: 10.1186/1471-2148-9-112 – volume: 536 start-page: 425 year: 2016 ident: 990_CR17 publication-title: Nature doi: 10.1038/nature19094 – volume: 537 start-page: 689 year: 2016 ident: 990_CR15 publication-title: Nature doi: 10.1038/nature19366 – volume: 5 start-page: 69 year: 2017 ident: 990_CR33 publication-title: Microbiome doi: 10.1186/s40168-017-0283-5 – ident: 990_CR37 doi: 10.1128/mSystems.00120-19 – volume: 34 start-page: 5839 year: 2006 ident: 990_CR69 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkl732 – volume: 34 start-page: 867 year: 2012 ident: 990_CR54 publication-title: BioEssays News Rev Mol Cell Dev Biol doi: 10.1002/bies.201200083 – volume: 9 start-page: 471 year: 2012 ident: 990_CR64 publication-title: Nat Methods doi: 10.1038/nmeth.1938 – volume: 15 start-page: 579 year: 2017 ident: 990_CR2 publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro.2017.87 – volume: 44 start-page: W16 year: 2016 ident: 990_CR30 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw387 – volume: 35 start-page: 436 year: 2013 ident: 990_CR8 publication-title: BioEssays doi: 10.1002/bies.201200174 – volume: 556 start-page: 197 year: 2018 ident: 990_CR25 publication-title: Nature doi: 10.1038/s41586-018-0012-7 – volume: 47 start-page: D427 year: 2019 ident: 990_CR43 publication-title: Nucleic Acids Res doi: 10.1093/nar/gky995 – volume: 18 start-page: 225 year: 1996 ident: 990_CR56 publication-title: FEMS Microbiol Rev doi: 10.1111/j.1574-6976.1996.tb00239.x – volume: 7 start-page: e1002195 year: 2011 ident: 990_CR42 publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1002195 – ident: 990_CR53 doi: 10.1101/836445 – volume: 89 start-page: 2459 year: 2015 ident: 990_CR11 publication-title: J Virol doi: 10.1128/JVI.03289-14 – ident: 990_CR70 – volume: 11 start-page: 119 year: 2010 ident: 990_CR41 publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-119 – volume: 11 start-page: 1710 year: 2020 ident: 990_CR26 publication-title: Nat Commun doi: 10.1038/s41467-020-15507-2 – ident: 990_CR40 doi: 10.1128/MMBR.00061-19 – volume: 44 start-page: D733 year: 2016 ident: 990_CR49 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkv1189 – volume: 24 start-page: 863 year: 2008 ident: 990_CR27 publication-title: Bioinforma Oxf Engl doi: 10.1093/bioinformatics/btn043 – volume: 49 start-page: 277 year: 2003 ident: 990_CR51 publication-title: Mol Microbiol doi: 10.1046/j.1365-2958.2003.03580.x – volume: 320 start-page: 1034 year: 2008 ident: 990_CR1 publication-title: Science doi: 10.1126/science.1153213 – volume: 202 start-page: e00052 issue: 9 year: 2020 ident: 990_CR14 publication-title: J Bacteriol doi: 10.1128/JB.00052-20 – volume: 177 start-page: 1109 year: 2019 ident: 990_CR16 publication-title: Cell doi: 10.1016/j.cell.2019.03.040 – volume: 46 start-page: D708 year: 2018 ident: 990_CR52 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkx932 – volume: 17 start-page: 383 year: 2019 ident: 990_CR3 publication-title: Nat Rev Microbiol doi: 10.1038/s41579-019-0191-8 – volume: 4 start-page: 1895 year: 2019 ident: 990_CR35 publication-title: Nat Microbiol doi: 10.1038/s41564-019-0510-x – volume: 37 start-page: 29 year: 2019 ident: 990_CR9 publication-title: Nat Biotechnol doi: 10.1038/nbt.4306 – ident: 990_CR67 doi: 10.1128/MRA.01325-18 – ident: 990_CR23 doi: 10.7554/eLife.05378 – volume: 13 start-page: 147 year: 2015 ident: 990_CR36 publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro3404 – volume: 32 start-page: 1792 year: 2004 ident: 990_CR65 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkh340 – volume: 348 start-page: 1261498 year: 2015 ident: 990_CR12 publication-title: Science doi: 10.1126/science.1261498 – volume: 5 start-page: e3428 year: 2017 ident: 990_CR38 publication-title: PeerJ doi: 10.7717/peerj.3428 – volume: 3 start-page: e985 year: 2015 ident: 990_CR29 publication-title: PeerJ doi: 10.7717/peerj.985 – volume: 8 start-page: 64 year: 2020 ident: 990_CR34 publication-title: Quant Biol doi: 10.1007/s40484-019-0187-4 – volume: 23 start-page: 205 year: 2009 ident: 990_CR66 publication-title: Genome Inf – volume: 96 start-page: 2192 year: 1999 ident: 990_CR13 publication-title: Proc Natl Acad Sci doi: 10.1073/pnas.96.5.2192 – volume: 40 start-page: e126 year: 2012 ident: 990_CR28 publication-title: Nucleic Acids Res doi: 10.1093/nar/gks406 – volume: 172 start-page: 1260 year: 2018 ident: 990_CR21 publication-title: Cell doi: 10.1016/j.cell.2017.10.045 – volume: 15 start-page: 475 year: 2018 ident: 990_CR71 publication-title: Nat Methods doi: 10.1038/s41592-018-0046-7 – volume: 47 start-page: D678 year: 2019 ident: 990_CR18 publication-title: Nucleic Acids Res doi: 10.1093/nar/gky1127 – volume: 540 start-page: 539 year: 2016 ident: 990_CR24 publication-title: Nature doi: 10.1038/nature20167 – volume: 35 start-page: 1026 year: 2017 ident: 990_CR60 publication-title: Nat Biotechnol doi: 10.1038/nbt.3988 – volume: 35 start-page: 725 year: 2017 ident: 990_CR6 publication-title: Nat Biotechnol doi: 10.1038/nbt.3893 – volume: 14 start-page: 508 year: 2016 ident: 990_CR4 publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro.2016.83 – volume: 6 start-page: eaay5981 year: 2020 ident: 990_CR45 publication-title: Sci Adv doi: 10.1126/sciadv.aay5981 – volume: 4 start-page: e08490 year: 2015 ident: 990_CR48 publication-title: eLife doi: 10.7554/eLife.08490 – volume: 578 start-page: 432 year: 2020 ident: 990_CR19 publication-title: Nature doi: 10.1038/s41586-020-1957-x – ident: 990_CR44 doi: 10.1128/JVI.00582-20 – volume: 12 start-page: 2825 year: 2011 ident: 990_CR50 publication-title: J Mach Learn Res – volume: 8 start-page: 858 year: 2017 ident: 990_CR46 publication-title: Nat Commun doi: 10.1038/s41467-017-01086-2 |
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Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence... Viruses are a significant player in many biosphere and human ecosystems, but most signals remain "hidden" in metagenomic/metatranscriptomic sequence datasets... Background Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence... Background : Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic... Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets... Abstract Background Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic... |
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| SubjectTerms | Bacteria BASIC BIOLOGICAL SCIENCES Bioinformatics Biomedical and Life Sciences Biomedicine Biosphere Deoxyribonucleic acid DNA DNA viruses DNA Viruses - classification DNA Viruses - genetics Earth Ecosystem Ecosystems Genes Genome, Viral - genetics Genomes Humans Identification Life Sciences Medical Microbiology Metagenomics Microbial Ecology Microbial Genetics and Genomics Microbiology Plasmids Proteins RNA polymerase RNA viruses RNA Viruses - classification RNA Viruses - genetics Software Software Article Virology Viruses |
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| Title | VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses |
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