Creation and Analysis of a Virome: Using CRISPR Spacers

Methods Mol Biol. 2015;1311:307-16. doi: 10.1007/978-1-4939-2687-9_20.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacteriophages / genetics*
  • Bacteriophages / physiology
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
  • Genomics*