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PSORTm

PSORTm is a bioinformatics tool 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.

Sequence sets of mixed organism and Gram stains must be provided along with an additional taxonomic classification file 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.

Please note there is also a PSORTm docker image available with a web interface at [***]

Installing this image

Warning: Users of this psortm 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 4GB space.

% sudo docker pull brinkmanlab/psortm_commandline:1.0.2

Once the Docker image has been installed, the following script can be installed to simplify the running of PSORTm analyses:

% wget [***]
% chmod +x psortm

Warning: Users of this psortm 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 PSORTm analysis

A PSORTm analysis can be run in the following way:

% ./psortm -h
% ./psortm -i [FASTA format sequence file] -t [comma-separated taxonomic classification file] -r [local results directory] [OPTIONS]

The taxonomic classification file must contain taxonomic classifications for all the sequences provided in comma-separated format. This file can be generated in a program such as MEGAN6.

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)

Versions

May 2017: Tag 1.0.0 - the first PSORTm 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.

License

PSORTm is distributed under GNU General Public License Version 3.

Support

Please email any questions to ***

This application was developed by Gemma Hoad in the Brinkman Laboratory at Simon Fraser University, Greater Vancouver, Canada.