FunBGCeX is a genome mining tool for fungal natural product discovery, which detects biosynthetic proteins based on our manually curated database of fungal natural product biosynthetic gene clusters (BGCs), FunBGCs. FunBGCeX can extract not only all possible BGCs from given fungal genomes but also those encoding a protein of user's interest. The extracted BGCs are provided in the GenBank format and can also be visualized using a web browser (You can access a sample output here or here).

Install the following dependencies:

• Python (version 3.8 or higher)
• DIAMOND (version 2.1.7 tested; older versions might cause database incompatibility)
• HMMER (version 3.3.2 tested)

Make sure that diamond and HMMER executables (e.g., hmmscan and hmmfetch) are on your system $PATH.
Note: FunBGCeX was tested on MacOS Ventura 13.4.

funbgcex can be installed using pip:

$ pip install funbgcex

or by cloning the repository and installing:

$ git clone https://github.com/ydmatsd/funbgcex.git
$ cd funbgcex/
$ pip install .

BGC extraction using funbgcex can be performed as follows:

$ funbgcex input_directory output_directory [options]

The input_directory is the path to a directory that contains GenBank files from which BGCs will be extracted. The GenBank files need to have CDS features with a translation qualifier. Do not include any non-GenBank files in the directory.
The output_directory is the path to a directory in which the results will be saved.

After the BGC extraction, the output directory should have the all_clusters and results directories and the CSV file named allBGCs.csv. The all_clusters directory contains all the extracted BGCs, while the results directory has separate results from each GenBank file. The CSV file allBGCs.csv contains the information of each extracted BGC.

To extract all possible BGCs from given fungal genomes, simply run without options as follows:

$ funbgcex input_directory output_directory

To extract BGCs that encode a homologue of protein(s) of your interest, use the target mode by specifying -m target. First, create a FASTA file containing the protein sequences, and then run the following:

$ funbgcex input_directory output_directory -m target -f FASTA_file

To extract BGCs that encode a protein with a protein family/domain (Pfam) of your interest, use the pfam mode by specifying -m pfam:

$ funbgcex input_directory output_directory -m pfam -p Pfam_name

See here for available protein domains.

Suppose you have several GenBank files in a directory named gbk in your current directory. If you wish to extract BGCs that encode a Pyr4-family terpene cyclase from these GenBank files and to obtain the result in a directory named results, then run the following:

$ funbgcex gbk results -m pfam -p Pyr4

Alternatively, you may prepare a FASTA file containing the protein sequences of Pyr4 homologues. If the FASTA file is saved as Pyr4.fasta (an example FASTA file can be found here) in your current directory, then run the following:

$ funbgcex gbk results -m target -f Pyr4.fasta

To check other options, run the following:

$ funbgcex --help

If you find FunBGCeX useful, please cite:
Tang, J., Matsuda, Y. Nat. Commun. 15, 4312 (2024)