PLAAC

Warning

PLAAC web server status: The PLAAC web server at plaac.wi.mit.edu is currently unavailable while it is being rebuilt. The rebuilt server will use modernized dependencies while retaining the existing overall look and feel. The underlying analysis code has also been updated, which results in some small changes to the ordering of COREScore rankings.

In the meantime, PLAAC can be run using the standalone command-line application. New packaged releases are available from the GitHub Releases page, including a self-contained JAR distribution and a Python wheel with a command-line interface. These packages are intended to make PLAAC easier to install and use without relying on the web server. See the command-line application documentation for details.

There is currently no estimated time for restoration. We will update this notice when the server is back online.

PLAAC (Prion-Like Amino Acid Composition) searches protein sequences to identify candidate prion subsequences using a hidden-Markov model (HMM) algorithm. The PLAAC website is located at:

http://plaac.wi.mit.edu/

This README.md file describes how to download, install and run standalone PLAAC, as well as developer instructions on how to compile from source and set up the web framework. PLAAC is released under the open-source MIT license.

Citing PLAAC

To cite use of either the PLAAC website or underlying code, in any publication, please cite Lancaster et al. (2014), which describes additional extensions and implementation details of the algorithm. Details of the PLAAC algorithm are described in Alberti et al. (2009) and also at http://plaac.wi.mit.edu/details.

• Alberti, S., Halfmann, R., King, O., Kapila, A., Lindquist, S. (2009) A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 137, 146–58.

• Lancaster, A.K., Nutter-Upham, A., Lindquist, King, O.D. (2014) PLAAC: a web and command-line application to identify proteins with Prion-Like Amino Acid Composition Bioinformatics doi:10.1093/bioinformatics/btu310

Command-line application (cli)

Installing a released package

Released versions of the PLAAC command-line application are available from the GitHub Releases page.

Each release provides two packages:

• plaac-v<VERSION>.zip — a self-contained command-line distribution containing the precompiled plaac.jar, example input, R plotting scripts, and documentation.
• plaac-<VERSION>-py3-none-any.whl — a Python package that provides a command-line interface to the same PLAAC Java application.

For most users who want to run PLAAC from the command line, the ZIP package is the simplest option.

Quick start: command-line ZIP package

1. Download the plaac-v<VERSION>.zip file from the GitHub Releases page.

2. Unpack the ZIP file:

   unzip plaac-v<VERSION>.zip
   

   This creates a directory named plaac-v<VERSION> containing the PLAAC application and supporting files.

3. Change into the unpacked directory:

   cd plaac-v<VERSION>
   

4. Check that Java 11 or later is installed:

   java -version
   

   If Java is not installed, it can be downloaded from java.com.

5. Run PLAAC using the example FASTA file included in the distribution:

   java -jar plaac.jar -i four_classic_prions.fasta
   

   This runs the command-line application using the included example input and writes the results to standard output.

To display the available command-line options, run:

   java -jar plaac.jar

The release package contains a precompiled version of PLAAC, so compiling the Java source code is not necessary for normal use.

More detailed instructions for the use of the plaac cli are found in cli/README.md.

Quick start: Python wheel

The Python wheel provides a Python package and command-line interface for PLAAC.

1. Download the plaac-<VERSION>-py3-none-any.whl file from the GitHub Releases page.

2. Install the downloaded wheel:

   python -m pip install plaac-<VERSION>-py3-none-any.whl
   

   You can also provide the path to the downloaded file if it is in another directory.

3. Use the PLAAC API wrapper as described in the Python wrapper documentation.

The Python package also requires Java 11 or later because the PLAAC application includes the Java implementation.

Building from source

Building PLAAC from source is primarily intended for developers and users who need to work with unreleased code or modify the PLAAC source. See cli/README.md for step-by-step details.

Note: PLAAC versions are derived from Git tags. Release builds use the Git/GitHub tag as the source of the version number, while development builds include information identifying the development version and Git commit.

Web-application

The web application is intended primarily for developers maintaining the PLAAC website, but can also be run by users who want to set up their own PLAAC web installation.

The web application uses the same compiled Java command-line application as the standalone CLI. For instructions on running, building, and deploying the web application, see web/README.md. These include:

• instructions for running the prebuilt container locally
• instructions for building and deploying the container on a server
• instructions for installing and running the web application directly from a git checkout for local development and testing