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Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "Isolation of cyanophages by liquid enrichment assay"
Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Propagation/Amplification of Lytic Agent. protocols.io dx.doi.org/10.17504/protocols.io.dq85zv Copy
Authors: Nick Tang
Group: VERVE Net, Upton-Lab
Summary: Viral Bioinformatic Resource CentreProvide databases of viral genomic information. Please check the Organisms menu to see which viruses we support: we’re now focusing on large DNA viruses
The VOCs (Virus Orthologous Clusters) database is at the heart of our system.
The database links directly to integrated tools for comparative analyses.
VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval.
Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (see VBRC Tools menu).
design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists.
Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations
Linking to research reviews/papers for the research community.
Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases
Building new features into our tools
Help with genome annotation
Proper citation: Nick Tang 2016. VBRC Base By Base: Switching between Mouse Modes. protocols.io dx.doi.org/10.17504/protocols.io.ecpbavn Copy
Authors: John H. Paul and Markus Weinbauer
Group: VERVE Net
Summary: This protocol gives a method for isolating temperate phages from marine viral concentrations. This protocol uses the conventional plaque agar overlay and looking for turbid or haloed plaques, a hallmark of temperate phages.Paul, J. H., and M. Weinbauer. 2010. Detection of lysogeny in marine environments, p. 30–33. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.Please see the full chapter for additional details.
Proper citation: John H. Paul and Markus Weinbauer 2016. Isolation of temperate phages by plaque agar overlay. protocols.io dx.doi.org/10.17504/protocols.io.dpd5i5 Copy
Authors: Ms Alex Aitken
Group: VERVE Net, Sullivan Lab
Summary: This shows how to make 1M Tris.
Proper citation: Ms Alex Aitken 2016. 1M Tris. protocols.io dx.doi.org/10.17504/protocols.io.c5vy65 Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines how to generate tables to analyze CRISPR interactions. Based on methods from the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.
Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script R16: CRISPR Analysis. protocols.io dx.doi.org/10.17504/protocols.io.ejqbcmw Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. Phenol extraction of Chlorella cells. protocols.io dx.doi.org/10.17504/protocols.io.eshbeb6 Copy
Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "One-step growth experiments (cyanophages)"
Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Remove unadsorbed phages. protocols.io dx.doi.org/10.17504/protocols.io.drb52m Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. Transformation of Bacterial Cultures Using Hexamine Cobalt Chloride. protocols.io dx.doi.org/10.17504/protocols.io.eq7bdzn Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol provides a method for detecting Human Polyomaviruses (HPyVs) in our virome and whole metagenome datasets. For genome reference, download the HPyV genomes (in fasta format) from NCBI (nucleotide) using the search terms "Human Polyomavirus" AND "Complete Genome". This is used in the rest of the analyses. Based on the methods from the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.
Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script P6: HPyV Detection. protocols.io dx.doi.org/10.17504/protocols.io.efxbbpn Copy
Authors: Rohan Sachdeva, Cheryl Chow
Group: VERVE Net, Fuhrman Lab
Summary: Reference: Fuhrman et al, 1988. Extraction from Natural Planktonic Microorganisms of DNA Suitable for Molecular Biological Studies. AEM 54(6), 1426‐1429
Proper citation: Rohan Sachdeva, Cheryl Chow 2015. SPOT DNA Extraction from 142mm Durapore 0.22µm Filters. protocols.io dx.doi.org/10.17504/protocols.io.dmi44d Copy
Authors: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith
Group: VERVE Net
Summary: This is a protocol from: Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7Please see the published manuscript for additional information.
Proper citation: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith 2016. Isolation of Haloviruses from Natural Waters. protocols.io dx.doi.org/10.17504/protocols.io.ebcbaiw Copy
Authors: Ken Stedman
Group: VERVE Net
Summary: For use in "PCTE Protocol for VLP enumeration"
Proper citation: Ken Stedman 2016. PCTE filter staining. protocols.io dx.doi.org/10.17504/protocols.io.eavbae6 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. 16S Universal Bacterial PCR. protocols.io dx.doi.org/10.17504/protocols.io.dfr3m5 Copy
Authors: HANNIGAN GC, GRICE EA, ET AL
Group: VERVE Net, Club Grice
Summary: This protocol provides a method for predicting the locations of the open reading frames (ORFs) using the Glimmer3 toolkit. Methods based on the publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.
Proper citation: HANNIGAN GC, GRICE EA, ET AL 2016. Script P3: Open Reading Frame Prediction. protocols.io dx.doi.org/10.17504/protocols.io.efpbbmn Copy
Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: Described is the procedure used to perform a onestep growth curve for cyanophage BBC1-P1 via plaque assay on Synechococcus sp. BBC1 (Suttle and Chan 1993).
Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. One-step growth experiments (cyanophages). protocols.io dx.doi.org/10.17504/protocols.io.dra52d Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Transcriptomics During One-Step Growth Curves for Cellulophaga Phages. protocols.io dx.doi.org/10.17504/protocols.io.dem3c5 Copy
Authors: Marine Phage Lab, Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Version 1b17 October 2012This protocol decribes the extraction of DNA from viral particles using Wizard Prep Resin and Columns from Promega.
Proper citation: Marine Phage Lab, Matthew Sullivan Lab 2016. DNA Extraction of Cesium Chloride-Purified Viruses using Wizard Prep Columns. protocols.io dx.doi.org/10.17504/protocols.io.c26yhd Copy
Authors: Bonnie Hurwitz, Ken Youens-Clark
Group: VERVE Net, Hurwitz Lab
Summary: K-mer-based approaches to determining sequence similiarity can be faster than traditional use of BLAST. This application uses Jellyfish to index host FASTA files, then uses the mode value (default 2) of the number of matching k-mers (default k=20) from the input sequence to determine whether the sequence is similar enough to the host sequence to be rejected. The output of the app is:"screened" directory containing the sequences from each file that were found to be dissimlar to the host"rejected" directory containing the sequence from each file that were too similar to the host"jf" directory containing Jellyfish indexes of each "host" file (useful for later runs with other files to skip recreating)"kmer" directory containing k-mers of query sequences and ".loc" file showing the number of ".kmer" lines associated to each sequence Code is freely available at Github.
Proper citation: Bonnie Hurwitz, Ken Youens-Clark 2016. K-mer-based host screening. protocols.io dx.doi.org/10.17504/protocols.io.ehjbb4n Copy
Authors: Bonnie Hurwitz, Ken Youens-Clark
Group: VERVE Net, Hurwitz Lab
Summary: Hurwitz, Bonnie L., and Matthew B. Sullivan. "The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology." PLoS One 8.2 (2013): e57355.
Proper citation: Bonnie Hurwitz, Ken Youens-Clark 2016. Running PCPipe (protein clustering) in iPlant. protocols.io dx.doi.org/10.17504/protocols.io.ef8bbrw Copy
Authors: William H. Wilson and Declan Schroeder
Group: VERVE Net
Summary: Generation of DNA fragments by DNase digestion involves digesting DNA for a range of times, then picking the time that gives optimal-sized DNA fragments (typically 1000–4000 bp).
Proper citation: William H. Wilson and Declan Schroeder 2016. Generation of DNA fragments by DNase digestion. protocols.io dx.doi.org/10.17504/protocols.io.dy47yv Copy
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