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HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

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dc.contributor University Of Hawaii Manoa
dc.contributor Div Computat Syst Biol
dc.contributor Univ Vienna
dc.contributor Ctr Microbial Oceanog Res & Educ
dc.contributor Univ Hawaii Manoa
dc.contributor Dept Microbiol & Ecosyst Sci
dc.contributor University Of Hawaii System
dc.contributor Sch Biosci
dc.contributor Univ Melbourne
dc.contributor University Of Vienna
dc.contributor Australian Inst Marine Sci
dc.contributor University Of Melbourne
dc.contributor Australian Institute Of Marine Science
dc.contributor.author RATTEI, THOMAS
dc.contributor.author LAFFY, PATRICK W.
dc.contributor.author WOOD-CHARLSON, ELISHA M.
dc.contributor.author TURAEV, DMITRIJ
dc.contributor.author WEYNBERG, KAREN D.
dc.contributor.author BOTTE, EMMANUELLE S.
dc.contributor.author VAN OPPEN, MADELEINE J. H.
dc.contributor.author WEBSTER, NICOLE S.
dc.date.accessioned 2017-03-21T01:03:51Z
dc.date.accessioned 2016-06-15T00:56:51Z
dc.date.accessioned 2016-06-15T00:56:51Z
dc.date.accessioned 2019-05-09T01:22:33Z
dc.date.available 2017-03-21T01:03:51Z
dc.date.available 2016-06-15T00:56:51Z
dc.date.available 2016-06-15T00:56:51Z
dc.date.available 2019-05-09T01:22:33Z
dc.date.issued 2016-06-09
dc.identifier.citation Laffy PW, Wood-Charlson E, Turaev D, Weynberg KD, Botte E, van Oppen MJH, Webster NS, Rattei T (2016) HoloVir: A workflow for investigating the diversity and function of viruses in invertebrate holobionts. Frontiers in Microbiology 7: 822 en_US
dc.identifier.issn 1664-302X
dc.identifier.uri http://epubs.aims.gov.au/11068/12761
dc.description.abstract Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora darnicomis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments.
dc.description.sponsorship NW was funded through an Australian Research Council Future Fellowship FT120100480. DT was supported by a PhD completion grant of the University of Vienna.
dc.description.sponsorship N.S.W. was funded through an Australian Research Council Future Fellowship 603 FT120100480. D.T. was supported by a PhD completion grant of the University of Vienna. en_US
dc.description.uri http://journal.frontiersin.org/article/10.3389/fmicb.2016.00822/abstract en_US
dc.language English
dc.language.iso en en_US
dc.publisher Frontiers - OPEN en_US
dc.relation.ispartof Null
dc.rights Attribution 3.0 Australia *
dc.rights.uri http://creativecommons.org/licenses/by/3.0/au/ *
dc.subject Bioinformatics Tools en_US
dc.subject Marine Invertebrates en_US
dc.subject Marine Ecology en_US
dc.subject Symbiosis en_US
dc.subject Host-associated Communities en_US
dc.subject Viral Metagenomics en_US
dc.subject Automated Tool
dc.subject Corals
dc.subject Genomes
dc.subject Microbiology
dc.subject Sequencing Data
dc.subject Viral Communities
dc.subject Particles
dc.subject Database
dc.subject Marine Viruses
dc.subject Metagenomic Data
dc.subject Annotation
dc.title HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts
dc.type journal article en_US
dc.identifier.doi 10.3389/fmicb.2016.00822
dc.identifier.wos WOS:000377358500001


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