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PSORTm

PSORTm is a standalone web application for predicting subcellular localization for a given set of protein sequences. The program has been designed to encourage analysis of metagenomic sequence sets containing archaea and bacteria of mixed or unknown Gram stain.

The entered set of sequences (required in FASTA format) is initially divided into bacteria of different Gram stains, archaea and sequences where organism type cannot be determined so that each set of sequences will receive more accurate localization predictions.

If your sequence set is of mixed organism and Gram stains, an additional taxonomic classification file is required to aid the sorting of the sequences. This file must be in csv format (reas, name or read, taxonomy-id), and can be generated by various programs such as Megan 6. See test input files for examples.

PSORTm is based on PSORTb version 3, with modifications. PSORTb is available at [***]

Please note that an alternative psortm docker image for command line use can be found at [***]

Source Code

This psortm docker image can be built from scratch from the code stored at [***]

Example Input Data

The following example PSORTm input files are available for download. These compressed files contain sequence files and MEGAN-generated taxonomy files:

• Windows ZIP file (242KB)
• Unix tar.gz file (62KB)

Installation

Please note docker commands often require sudo access, depending on your system setup. Therefore the following commands have been prefixed with the sudo command in case your system requires it.

To install and run PSORTm docker image, run the following commands. First, download the Docker Hub image:

sh
$ sudo docker pull brinkmanlab/psortm:1.0.2  

  Secondly, to run the image and set up the website, use the following commands. Ensure you substitute [/path/to/store/result] twice in the following command with a locally accessible path where you would like to save your results files.

sh
$ sudo docker run -d -p 80:80 -v [/path/to/store/results]:/tmp/psortm -e NODE_ENVIRONMENT="production" -e MOUNT_DIRECTORY="[/path/to/store/results]" --restart=always --name psortm brinkmanlab/psortm:1.0.2  

  If you have a preference for a different port number e.g. port 3000, use option -p 3000:80 .

After running these commands, PSORTm can be accessed from an internet browser which sits locally to the running image, by going to http://localhost (default port 80) or http://localhost:[port number] if you chose to use a different port in the docker run command.

Versions

May 2017: Tag 1.0.0 - the first PSORTm Docker image release.
Dec 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.

License

PSORTm is distributed under GNU General Public License Version 3.

Software History

May 5, 2017 Version 1.0 of the PSORTm docker image has been developed in the Brinkman Laboratory using code from PSORTb docker which was previously developed by Matthew Laird. Publication: Hoad and Brinkman, unpublished PSORTb 3.0 publication: Yu and Brinkman, 2010

December 8, 2017 Version 1.0.1 release of the PSORTm docker image. This image contains 32 additional sequences in the subcellular localization blast data sets (see the PSORTdb paper for details).

Jun 13, 2018 Version 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.

About

PSORTm has been put together by Gemma Hoad of the Brinkman Laboratory at Simon Fraser University, Burnaby, British Columbia, Canada with the invaluable help of Mike Peabody, Claire Bertelli, Geoff Winsor, Matthew Laird, Fiona Brinkman and the Research Computing group.

Contact

Please contact *** with any questions. We will be happy to help.