Fig. 1
An overview of the BOA Pipeline. The stages in the pipeline are elaborated upon in the ‘Methods’ section. (1): construction of the LC-Set and the BAGEL set; (2) BLAST LC and BAGEL genes against all bacterial & archaeal genomes evalue= 10−5; (3) select the ORFs within ±50 kb of homologs to toxin genes (4) assign ORFs to one of the following classes (left to right): toxin, modifier, immunity, transport, regulation; (5) build pHMMs from each category: cluster sequences using CD-HIT, align sequences in each cluster using MAFFT, then use hmmbuild from the HMMER suite to construct HMMs; (6) run hmmsearch from the HMMER suite against the genome files to extract more sequences from each category, remove predicted false positives using a threshold score as explained in Methods (7) use a clique filter to identify genes that are close together