Fig. 1

Description of the computational pipeline used to detect attC sites in metagenomic data. Assembled metagenomic DNA sequences are used as input. Next, the gHMM-based HattCI is used to detect the attC sites present in the input sequences. Subsequently, the secondary structure of the detected attC sites is evaluated by a covariance model implemented in Infernal, which runs the search in its most sensitive mode. Identified attC sites on the same strand are considered to be part of the same integron when they are at maximum 4,000 nucleotides (nt) apart. Note that integrons with only one attC site are removed from the analysis in order to ensure a high true positive rate. Finally, the ORFs are predicted upstream of the attC sites