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Creation and Analysis of a Virome: Using CRISPR Spacers

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CRISPR

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1311))

Abstract

Advances in sequencing technology have allowed for the study of complex and previously unexplored microbial and viral populations; however, linking host–phage partners using in silico techniques has been challenging. Here, we describe the flow-through for creation of a virome, and its subsequent analysis with the viral assembly and analysis module “Viritas,” which we have recently developed. This module allows for binning of contigs based on tetranucleotide frequencies, putative phage-host partner identification by CRISPR spacer matching, and identification of ORFs.

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Acknowledgments

DB acknowledges funding support from the NSF (MCB#1024755) and the Carnegie Institution of Science. This protocol is a modification of the Viritas pipeline described in Davison et al (in prep) which was carried out in collaboration with Mihai Pop, a the University of Maryland and his group. Viritas has been incorporated into the metAMOS pipeline (https://github.com/marbl/metAMOS).

Author information

Authors and Affiliations

  1. Department of Plant Biology, Carnegie Institution for Science, Stanford University, 260 Panama Street, Stanford, CA, 94305, USA

    Michelle Davison & Devaki Bhaya

Authors
  1. Michelle Davison
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  2. Devaki Bhaya
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Corresponding author

Correspondence to Devaki Bhaya .

Editor information

Editors and Affiliations

  1. Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

    Magnus Lundgren

  2. Department of Molecular Biology MIMS, Umeå University, Umeå, Sweden

    Emmanuelle Charpentier

  3. Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand

    Peter C. Fineran

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Davison, M., Bhaya, D. (2015). Creation and Analysis of a Virome: Using CRISPR Spacers. In: Lundgren, M., Charpentier, E., Fineran, P. (eds) CRISPR. Methods in Molecular Biology, vol 1311. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2687-9_20

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  • DOI: https://doi.org/10.1007/978-1-4939-2687-9_20

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2686-2

  • Online ISBN: 978-1-4939-2687-9

  • eBook Packages: Springer Protocols

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