jaroszlab / plaac

Prion-Like Amino Acid Composition

PLAAC

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 file is for developers and others interested in accessing the Java code and the web framework, which 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

Installation

Command-line application (cli)

cd cli
./build_plaac.sh

This will build a plaac.jar file , as well as column outputs for the website in the _plaac_headers.haml both in the cli/target subdirectory. More detailed instructions for the use of the plaac cli are found in cli/README.md.

Web-application

Perform the same steps as for the cli, above, then:

cp target/plaac.jar ../web/bin/
cp R/plaac_plot.r R/plaac_plot_util.r ../web/bin/

If the column outputs from cli version have changed (i.e. in cli/src/plaac.java), you will also need to update the HAML code for the website:

cp target/_plaac_headers.haml ../web/views/

The remaining installation steps are detailed in the web/README.md (note that Rscript should be installed).