TAtouScan

TAtouScan is a command-line tool designed to identify toxin-antitoxin (TA) systems in genomes and metagenomes.

Installation

Option 1: Install with pip

1. Clone the repository:

git clone https://github.com/JeanMainguy/TAtouScan.git
cd TAtouScan

2. Create and activate a virtual environment:

# Create a virtual environment
python -m venv venv

# Activate the virtual environment
# On Linux/macOS:
source venv/bin/activate

1. Install TAtouScan:

pip install .

---

Option 2: Install using conda

If you prefer using conda, you can create a dedicated environment as follows:

# Create a new conda environment with Python
conda create -n tatouscan python=3.12

# Activate the environment
conda activate tatouscan

# Clone the repository
git clone https://github.com/JeanMainguy/TAtouScan.git
cd TAtouScan

# Install TAtouScan
pip install -e .

Note

TAtouScan is not yet available via bioconda. The above method combines conda for environment management and pip for installation.

Download TAtouScan HMM Database

TAtouScan requires a database of HMM profiles to run. You can download the latest version from Zenodo:
🔗 https://zenodo.org/records/15305313

Download the required files using:

wget https://zenodo.org/records/15305313/files/tatouscan_hmm_description.tsv
wget https://zenodo.org/records/15305313/files/tatouscan_hmm_profiles.hmm.gz

Usage

After installation and downloading the required HMM database, you can run TAtouScan as follows:

TAtouScan currently requires:

• a GFF file with gene annotations
• a FAA file with the corresponding protein sequences

To identify toxin-antitoxin systems in a genome, run:

tatouscan --gff <genes.gff> --faa <proteins.faa> \
  --hmm_db tatouscan_hmm_profiles.hmm.gz \
  --hmm_info tatouscan_hmm_description.tsv

This command will produce an output file named:
📄 tatouscan_results.tsv — listing all predicted toxins and antitoxins found in the input genome.

HMM Database Composition

The HMM database used by TAtouScan is composed of profiles collected from multiple sources, including curated databases and literature. The file tatouscan_hmm_description.tsv provides metadata for each profile, indicating its origin and whether it corresponds to a toxin or an antitoxin.

Breakdown of the database:

• 682 profiles were obtained from the TASmania project:

  Akarsu H, Bordes P, Mansour M, Bigot D-J, Genevaux P, Falquet L (2019). TASmania: A bacterial Toxin-Antitoxin Systems database. PLoS Comput Biol 15(4): e1006946.
  https://doi.org/10.1371/journal.pcbi.1006946

• 3,168 profiles were generated from sequences in the TADB 3.0 database:
  These sequences were first clustered, and each cluster was then aligned using multiple sequence alignment. HMM profiles were built from the resulting alignments.

  Guan J, Chen Y, Goh YX, Wang M, Tai C, Deng Z, Song J, Ou HY (2024).
  TADB 3.0: an updated database of bacterial toxin-antitoxin loci and associated mobile genetic elements.
  Nucleic Acids Research, 52(D1): D784–D790.
  https://doi.org/10.1093/nar/gkad962

• Additional HMM profiles were manually collected from other sources in the literature.

Output

TatouScan produces a TSV file (tatouscan_results.tsv) summarizing the predicted toxin-antitoxin (TA) genes. The file includes the following columns:

Column Name	Description
contig_name	Name of the contig where the gene is located
gene_id	Unique identifier of the gene (from the input GFF file)
start	Start position of the gene on the contig
end	End position of the gene on the contig
strand	Strand of the gene (+ or -)
product	Predicted function or product of the gene (if available)
is_single_gene	Whether the gene is a single hit or part of a TA pair (True/False)
ta_system_id	ID of the TA system this gene belongs to (shared between paired genes)
gene_type	Type of gene: either toxin or antitoxin
TASmania_hmm_name	Name of the matched HMM profile from the TASmania database (if any)
TASmania_hmm_score	Bit score of the TASmania HMM hit
TASmania_hmm_evalue	E-value of the TASmania HMM hit
TASmania_hmm_description	Description of the TASmania HMM profile
Other_hmm_name	Name of a matched HMM profile from other sources (if any)
Other_hmm_score	Bit score of the "Other" HMM hit
Other_hmm_evalue	E-value of the "Other" HMM hit
Other_hmm_description	Description of the HMM profile from other sources
TADB3_hmm_name	Name of the matched HMM profile from the TADB3 database (if any)
TADB3_hmm_score	Bit score of the TADB3 HMM hit
TADB3_hmm_evalue	E-value of the TADB3 HMM hit
TADB3_hmm_description	Description of the TADB3 HMM profile

License

This project is licensed under the MIT License.