Localizer

Overview

Localizer is a machine learning method for subcellular localization prediction in plant cells. LOCALIZER has been trained to predict either the localization of plant proteins or the localization of eukaryotic effector proteins to chloroplasts, mitochondria or nuclei in the plant cell.

The localization to chloroplasts and mitochondria is predicted using the presence of transit peptides and the localization to nuclei is predicted using a collection of nuclear localization signals (NLSs).

Using

Use the module name localizer to discover versions available and to load the application. Localizer is written in python and runs using the LOCALIZER.py command. The localizer command may be run with a few specific flags:

-e      : sets effector mode
-p      : sets plant mode
-i      : indicates the string that follows is the path to the file on which we are performing the prediction.
-M      : in effector mode, do not remove the signal peptide. Use this if you are providing mature effector sequences.
-S <x>  : in effector mode, remove the signal peptide by deleting the first x aas (default: 20).

Before calling LOCALIZER.py, run . setup.sh to ensure proper directories are made available to the version of biopython on which Localizer is dependent.

Example:

module load localizer/version#

...

. setup.sh
python LOCALIZER.py -e -i path/to/file/test_file.fasta

...