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Clustered regularly interspaced short palindromic repeats (CRISPR) constitute a bacterial and archaeal adaptive immune system that protect against bacteriophage (phage). Analysis of CRISPR loci reveals the history of phage infections and provides a direct link between phage and their hosts.
(Skennertonet al., 2013) Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Res.