This repository provides a Docker container that wraps the PSORTb program for bacterial protein subcellular localization prediction.

PSORTb is available at https://psort.org/psortb/.

PSORTb binaries are available at https://github.com/brinkmanlab/psortb_commandline_docker.

• Run PSORTb easily without manual installation.
• Predict subcellular localization for bacterial proteins.
• Input/output handled via mounted directories for easy access.

Clone this repository:

git clone https://github.com/labioinfoufsc/PSORTb.git

Build the Docker image from scratch (optional; image also available on Docker Hub):

docker build -t bioinfoufsc/psortb -f PSORTb/Dockerfile PSORTb/ 

See the params:

docker run --rm bioinfoufsc/psortb -h

Run the first 100 proteins of the Clostridium botulinum proteome:

docker run --rm -v ${PWD}/PSORTb:/data/ bioinfoufsc/psortb -p -o terse -i /data/examples/gram_positive.fasta -r /data/examples/gram_positive.txt

Run the first 100 proteins of the Borreliella burgdorferi proteome:

docker run --rm -v ${PWD}/PSORTb:/data/ bioinfoufsc/psortb -n -o terse -i /data/examples/gram_negative.fasta -r /data/examples/gram_negative.txt

Notes:

• ${PWD}/PSORTb mounts your local PSORTb directory to /data/ inside the container.
• Input FASTA files should be placed in /data/examples/.
• Output results will be saved in /data/examples/.

If you use PSORTb in your work, please cite:

PSORTb v3.0
N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao, S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010).
PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
Bioinformatics, 26(13): 1608–1615.
https://doi.org/10.1093/bioinformatics/btq249

PSORTb Docker Wrapper is part of the FastProtein project
👉 https://github.com/labioinfoufsc/FastProtein

If this utility has been useful in your research or contributed in any way to your work, please cite the repository and the following publication:

Moreira RS, Benetti Filho V, Maia GA, Soratto TAT, Kawagoe EK, Russi BC, Miletti LC, Wagner G.
FastProtein—an automated software for in silico proteomic analysis.
PeerJ 12:e18309 (2024).
https://doi.org/10.7717/peerj.18309

👉 Repository: https://github.com/bioinfoufsc/PSORTb

• The Docker image bundles PSORTb for Linux and sets up the environment automatically.
• Ensure your input FASTA files exist in the directory mounted to /data/.
• Output files will be accessible on your host system through the same mounted directory.
• This wrapper simplifies running PSORTb without installing Perl, Bioperl, or other dependencies manually.