PSORTb is a bioinformatics tool for predicting subcellular
localization for a given set of protein sequences. The protein
sequences must belong to one type of organisms, classified by
cell membrane type in order to more accurately predict subcellular
localization. The supported organism types are:
- Gram negative (-n)
- Gram positive (-p)
- archaea (-a)
- Gram negative without outer membrane
- Gram positive with outer membrane
The PSORTb program has been added to a Docker container to
simply the installation process.
This PSORTb installation uses PSORTb version 3.
Installing this image
Warning: Users of this psortb app must have admin rights to run docker commands. Either that or an administrator must give you access to run "docker run" commands.
This image takes up 2.55GB space.
% sudo docker pull brinkmanlab/psortb_commandline:1.0.2
Once the Docker image has been installed, the following script can be installed to simplify the running of PSORTb analyses:
% wget https://raw.githubusercontent.com/brinkmanlab/psortb_commandline_docker/master/psortb % chmod +x psortb
Warning: Users of this psortb app must have admin rights to run docker commands. Either that or an administator must give you access to run "docker run" commands.
Running a PSORTb analysis
Once the Docker image has been installed, run an PSORTb analysis like this:
% ./psortb -h % ./psortb -i <FASTA format sequence file> -r <local results directory> [--positive|--negative|--archaea]
For administrators wanting to tweak the Docker setup, the Dockerfile used to build this image can be found on GitHub:
The Dockerfile builds the complex environment of PSORTb. The repository also contains
a wrapper script (named psortb) to run the PSORTb analysis inside the
Docker container (i.e a wrapper for the "docker run" command).
Warning: Users of this app must have admin rights to run docker commands.
Either that or an administrator must give you access to run "docker run"
Jun 2017: Tag 1.0.0 - the first PSORTb command line Docker image release.
Nov 2017: Tag 1.0.1 contains an additional 32 sequences in the subcellular localization blast data sets (see the PSORTdb paper for details).
Jun 2018: Tag 1.0.2 contains a bug fix which addresses a change in Bioperl and ensures input sequences entered in lower case give the same results to those entered in upper case.
PSORTb is distributed under GNU General Public License Version 3.
Please email any questions to firstname.lastname@example.org
This application was developed by Gemma Hoad of the Brinkman Laboratory at Simon Fraser University, Greater Vancouver, Canada.