Biosynthetic gene clusters (BGCs) in Lactobacillaceae

1.BGC prediction

#GENOME.FA epresents input in fasta format
antismash GENOME.FA --taxon bacteria --output-dir PATH OF OUTPUT --genefinding-tool prodigal --cb-knownclusters -c 20 --cc-mibig --fullhmmer
#
batch_extract_antismash_json_v2.py

2.BiG-SCAPE

#GCF analysis on a default score cutoff (c=0.3)
python bigscape.py -i gbk.files -o CGF.out --pfam_dir PFAM.db –cutoffs 0.3 -c 60 --include_singletons --mode auto
#GCF analysis on different cutoffs (c=0.5 and c=0.7)
python bigscape.py -i gbk.files -o CGF.out --pfam_dir PFAM.db –cutoffs 0.5 0.7 -c 60 --include_singletons --mode auto --mix --no_classify

3.Extraction of precursor peptide

#The precursor peptide, including leader and core peptide regions, are obtained from gbk files using "extract_peptides.py" located in the scripts/ directory

extract_peptides.py

4.Prediction of metabolites produced by BGCs

#“--cb-knownclusters” option is used to compare our BGC sequences against the MIBiG database
antismash 02.rep.BGC/${i}.gbk --taxon bacteria --output-dir out/${i} --genefinding-tool prodigal --cb-knownclusters -c 2 --cc-mibig --fullhmmer
#Extract antismash annotation results
python batch_extract_antismash_json_v2.py -i JSON.files -o result.xlsx
#BiG-SCAPE annotation uing "--mibig"option
python ./bigscape.py -i ./02.rep.BGC -o BiG-SCAPE.out --pfam_dir ./BiG-SCAPE-master/ -c 60 --cutoffs 0.3 --include_singletons --mode auto --mix --no_classify --mibig

5.BiG-SLiCE

#The BGC files in gbk format are organized into the input folder according to the developer's requirements (https://github.com/medema-group/bigslice), "bigslice_2.0.0_T0.4_16April" is downloaded from BGC Atlas database.

bigslice --query BGC/ --n_ranks 1 bigslice_2.0.0_T0.4_16April -t 60

6.BGC_function_prediction

#run with Resistance Gene Identifier (RGI)
rgi main --input_sequence bgc_fasta.file --output_file bgc.rgi --input_type contig --local --clean -n 1
#
./cluster_function_prediction.py ./gbk.files ./bgc.rgi --output ./BGC_function_prediction --antismash_version 5 --rgi_version 5