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| Name | Authors | DOI | Group |
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Associated Publications |
RRIDs used | ||||||
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PCPipe: Protein clustering with SIMAP annotations Resource Report Resource Website |
Bonnie Hurwitz, Ken Youens-Clark | DOI:10.17504/protocols.io.ehfbb3n | VERVE Net, Hurwitz Lab | PCPipe is a protein-clustering tool. The input is a set of ORFs and a FASTA file with already clustered ORFs. The process entails:Use cd-hit-2d to compare the input peptides to previously clustered proteinsThe result is a file with input proteins that clustered to existing clusters and those that did notUse the unclustered peptides and self-cluster them via cd-hitTake a representative sequence from each novel cluster, and use "blastp" to compare to SIMAP.Use the resulting SIMAP "feature_id" to look up the SIMAP features, merging the query results with the protein ID into a tab-delimited annotations fileProvide the user with two cluster files and the annotations for the new clusters based on the representative sequenceCode is freely available at Github. | University of Arizona, University of Arizona | 1 | 2016 | Bonnie Hurwitz, Ken Youens-Clark 2016. PCPipe: Protein clustering with SIMAP annotations. protocols.io https://dx.doi.org/10.17504/protocols.io.ehfbb3n | 2021-04-15 09:16:51 | |||
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Filtering for Cell Collection Resource Report Resource Website |
SangHoon Lee | DOI:10.17504/protocols.io.dmb42m | VERVE Net, Fuhrman Lab | Filtering protocol adapted from SangHoon Lee | Fuhrman Lab | 1 | 2015 | SangHoon Lee 2015. Filtering for Cell Collection. protocols.io https://dx.doi.org/10.17504/protocols.io.dmb42m | 2021-04-15 09:17:00 | |||
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Installation and Getting Started Resource Report Resource Website |
Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. | DOI:10.17504/protocols.io.d5k84v | VERVE Net, Hurwitz Lab | Motivation: An important step of "metagenomics" analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines employ a single-genome assembler with carefully optimized parameters and post-process the resulting scaffolds to correct assembly errors. Limitations of the use of a single-genome assembler for de novo metagenome assembly are that highly conserved sequences shared between different species often causes chimera contigs, and sequences of highly abundant species are likely mis-identified as repeats in a single genome.Methods:We modified and extended a single-genome and de Bruijn-graph based assembler, Velvet, for de novo metagenome assembly. Our fundamental ideas are first decomposing de Bruijn graph constructed from mixed short reads into individual sub-graphs and second building scaffolds based on every decomposed de Bruijn sub-graph as isolate species genome. | Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab | http://metavelvet.dna.bio.keio.ac.jp/MV.html | 1 | 2016 | Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2016. Installation and Getting Started. protocols.io https://dx.doi.org/10.17504/protocols.io.d5k84v | 2021-04-15 09:16:56 | ||
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Chlorovirus Purification Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.er2bd8e | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Chlorovirus Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.er2bd8e | 2021-04-15 09:16:58 | ||||
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Amplification of phage genes from lysates and environmental samples Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.djn4md | VERVE Net, Sullivan Lab | From Sullivan M., Lindell D., Lee J., Thompson L., Bielawski J., Chisholm S. Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts.PLOS Biology, 2006 4(8):e234. Please see the published manuscript for additional information. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Amplification of phage genes from lysates and environmental samples. protocols.io https://dx.doi.org/10.17504/protocols.io.djn4md | 2021-04-15 09:16:52 | |||
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Eisen Lab, Fresh Cow Dung Resource Report Resource Website |
Emily E. Hare, Brant K. Peterson, Venky N. Iyer, Rudolph Meier, Michael B. Eisen | DOI:10.17504/protocols.io.ebebaje | VERVE Net | This protocol is from:Hare EE, Peterson BK, Iyer VN, Meier R, Eisen MB (2008) Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation. PLoS Genet 4(6): e1000106. doi:10.1371/journal.pgen.1000106Please see the full manuscript for additional details.(Image: calf, Jim Champion, CC BY-SA) | Eisen Lab, Eisen Lab, Eisen Lab, Eisen Lab, Eisen Lab | http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000106 | 1 | 2015 | Emily E. Hare, Brant K. Peterson, Venky N. Iyer, Rudolph Meier, Michael B. Eisen 2015. Eisen Lab, Fresh Cow Dung. protocols.io https://dx.doi.org/10.17504/protocols.io.ebebaje | 2021-04-15 09:17:04 | ||
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Lysozyme & RNase A Solution Resource Report Resource Website |
DeLong Lab | DOI:10.17504/protocols.io.dje4jd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | DeLong Lab 2015. Lysozyme & RNase A Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dje4jd | 2021-04-15 09:17:03 | ||||
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Preparation of Virus DNA from Seawater for Metagenomics Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c28yhv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Matthew Sullivan Lab 2016. Preparation of Virus DNA from Seawater for Metagenomics. protocols.io https://dx.doi.org/10.17504/protocols.io.c28yhv | 2021-04-15 09:17:04 | ||||
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9 ?L reaction mix Resource Report Resource Website |
Karen D. Weynberg, Elisha M. Wood-Charlson, Curtis A. Suttle, and Madeleine J. H. van Oppen | DOI:10.17504/protocols.io.emcbc2w | VERVE Net | For use in Generating viral metagenomes from the coral holobiont. | , , , | 1 | 2016 | Karen D. Weynberg, Elisha M. Wood-Charlson, Curtis A. Suttle, and Madeleine J. H. van Oppen 2016. 9 ?L reaction mix. protocols.io https://dx.doi.org/10.17504/protocols.io.emcbc2w | 2021-04-15 09:17:06 | |||
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Virus Purification by Sucrose Density Gradients Resource Report Resource Website |
Steven Wilhelm | DOI:10.17504/protocols.io.grzbv76 | VERVE Net, The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Samantha R Coy's Protocols | Adapted from: Van Etten, J. (n.d.). Titering of Chlorella Viruses. Retrieved from http://ncv.unl.edu/vanettenlab/ | The University of Tennessee, Knoxville | http://ncv.unl.edu/vanettenlab/Chlorovirus%20Purification.pdf | 1 | 2016 | Steven Wilhelm 2016. Virus Purification by Sucrose Density Gradients. protocols.io https://dx.doi.org/10.17504/protocols.io.grzbv76 | 2021-04-15 09:17:07 | ||
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Urea Solution Resource Report Resource Website |
Kristin Corrier/Nathan VerBerkmoes | DOI:10.17504/protocols.io.dei3cd | VERVE Net, Sullivan Lab | For use in 'FASP Kit Protocol-ORNL Developed for Bacteriophage' | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Kristin Corrier/Nathan VerBerkmoes 2016. Urea Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dei3cd | 2021-04-15 09:17:07 | |||
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Concentrating Viruses via PEG precipitation Resource Report Resource Website |
Jozef Nissimov | DOI:10.17504/protocols.io.d9j94m | VERVE Net, Bidle Lab | Concentrating Viruses via PEG precipitation | DMCS, Rutgers University | 1 | 2015 | Jozef Nissimov 2015. Concentrating Viruses via PEG precipitation. protocols.io https://dx.doi.org/10.17504/protocols.io.d9j94m | 2021-04-15 09:14:22 | |||
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FLVP assays Resource Report Resource Website |
André M. Comeau and Rachel T. Noble | DOI:10.17504/protocols.io.dzr755 | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | The following continued adaptation of Hennes et al. (1995) is a result of FLVP assay optimizations for the Vibrio alginolyticus PWH3a-phage P1 phage-host system (PHS) for use with SYBR Green I stain. Novices to microscopy would benefit from reading Wen et al. (2004) for details on preparing and storing slides using SYBR Green I stain. This protocol is a modification of the standard slide preparation techniques for bacteria and viruses in aquatic samples (see Suttle and Fuhrman 2010, this volume). | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_019.pdf | 1 | 2016 | André M. Comeau and Rachel T. Noble 2016. FLVP assays. protocols.io https://dx.doi.org/10.17504/protocols.io.dzr755 | 2021-04-15 09:14:23 | ||
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Preparation and application of fluorescently labeled virus particles Resource Report Resource Website |
André M. Comeau and Rachel T. Noble | DOI:10.17504/protocols.io.d2q8dv | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | Comeau, A. M., and R. T. Noble. 2010. Preparation and application of fluorescently labeled virus particles, p. 19–29. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.Please see the published manuscript for additional information. | 1 | 2016 | André M. Comeau and Rachel T. Noble 2016. Preparation and application of fluorescently labeled virus particles. protocols.io https://dx.doi.org/10.17504/protocols.io.d2q8dv | 2021-04-15 09:14:21 | ||||
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0.7% Agarose Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c7bzim | VERVE Net, Sullivan Lab | . | 1 | 2016 | Matthew Sullivan 2016. 0.7% Agarose. protocols.io https://dx.doi.org/10.17504/protocols.io.c7bzim | 2021-04-15 09:14:24 | ||||
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Cellulophaga Media Recipes Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dez3f5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Cellulophaga Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.dez3f5 | 2021-04-15 09:14:27 | ||||
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CviRI Buffer C Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.esybefw | VERVE Net | For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviRI Buffer C. protocols.io https://dx.doi.org/10.17504/protocols.io.esybefw | 2021-04-15 09:14:28 | ||||
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FASP Kit Protocol-ORNL Developed for Bacteriophage Resource Report Resource Website |
Nathan VerBerkmoes | DOI:10.17504/protocols.io.ddn25d | VERVE Net, Sullivan Lab | Collaborator, Nathan VerBerkmoes (Oak Ridge National Labs), worked with Tucson Marine Phage Lab to develop more sensitive proteomics assays for viral isolates which we are now also using for environmental viral concentrates. A new sample prep method (FASP) was optimized to maximize the signal from our commonly low-protein containing samples, and then run using 2d-LC-MS-MS to maximize detection across the large dynamic range in isolate and environmental samples. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Nathan VerBerkmoes 2016. FASP Kit Protocol-ORNL Developed for Bacteriophage. protocols.io https://dx.doi.org/10.17504/protocols.io.ddn25d | 2021-04-15 09:14:23 | |||
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Silver Development protocol (silver stain) for 0.75mm polyacrylamide gels Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.ermbd46 | VERVE Net | University of Nebraska-Lincoln | http://lclane.net/text/agstain.html | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Silver Development protocol (silver stain) for 0.75mm polyacrylamide gels. protocols.io https://dx.doi.org/10.17504/protocols.io.ermbd46 | 2021-04-15 09:14:35 | |||
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VIROME: Downloading libraries of VIROME data Resource Report Resource Website |
Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack | DOI:10.17504/protocols.io.d5m845 | VERVE Net, Hurwitz Lab | This tutorial explains how to download entire libraries of data from the VIROME web application. Wommack, K. E., J. Bhavsar, S. W. Polson, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar, and D. J. Nasko. 2012. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Standards in Genomic Sciences 6:427-439 [PMC3558967] See site for more information. | University of Arizona, University of Arizona, University of Arizona | http://virome.dbi.udel.edu/ | 1 | 2016 | Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack 2016. VIROME: Downloading libraries of VIROME data. protocols.io https://dx.doi.org/10.17504/protocols.io.d5m845 | 2021-04-15 09:14:27 |
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