Computational protocol: Foreign DNA acquisition by the I-F CRISPR–Cas system requires all components of the interference machinery

Similar protocols

Protocol publication

[…] High-throughput sequence analysis was made with MiSeq Illumina system. The data were preprocessed and analyzed using ShortRead () and BioStrings () Bioconductor packages. Sequences located between two CRISPR repeats were considered as spacers. They were mapped on genome and all plasmids presented in the certain sample with no mismatches allowed. To assign non-unique spacers from common regions of pCas and pCsy plasmids the following procedure was used. First, spacers originating from unique regions of each plasmid were counted. The ratio of the number of such unique spacers, normalized for the length of each plasmid, was taken as a measure of mean spacer acquisition efficiency from each plasmid. The non-unique spacers that could have originated from either plasmid were next assigned to either pCas or pCsy based on this measure. R scripts were used for statistical analysis and Circos () was used for graphical representation of the data. […]

Pipeline specifications

Software tools ShortRead, Biostrings, Circos
Application Genome data visualization