EffectiveT3

Download the Effective core software:
TTSS_GUI-1.0.1.jar

Download the Effective classification modules:
TTSS_STD-2.0.1.jar     (based on all training data; 09/2015)
TTSS_STD-1.0.1.jar     (based on all training data; 08/2009)
TTSS_ANIMAL-1.0.1.jar  (based on training data from human/animal-associated bacteria; 08/2009)
TTSS_PLANT-1.0.1.jar   (based on training data from plant-associated bacteria; 08/2009)

Installation instructions

Prerequisites:
SUN Java 1.5 or higher (Java 2 Standard Edition is sufficient)

Installation:

    Download the Effective core software (typically the latest version) to a folder of your choice (this will be the program folder).
    Create a folder named "module" as subfolder of the program folder (this will be the module folder).
    Download all Effective classification modules (typically the latest versions) you want to use into the module folder.


Usage:
1) Prediction of a single sequence

    Run the Effective core software TTSS_GUI.jar by double clicking
    Paste the query amino acid sequences without any header and line numbers into the sequence window
    Click "Next"
    Adjust or enter the score threshold (score corresponds to probability of secretion) and select a training set
    Click "Next"
    Results are displayed and can be saved into a text file

2) Prediction of a set of sequences

    Run TTSS_GUI.jar by double clicking
    Click "Load file"
    Adjust the filename suffix filter, browse and select the multiple fasta file containing query sequences (in the current version only amino acid sequences can be used)
    Click "Next"
    Adjust or enter the score threshold (score corresponds to probability of secretion) and select a training set
    Click "Next"
    Results are displayed and can be saved into a text file


Output format:
The table of results displays all query proteins sorted by prediction score. Effector classification (true/false) according to the applied threshold is shown in the last column.

Command line usage:
Running TTSS_GUI.jar in a terminal or command line window with the option --help will list the options for command line usage. The command line is triggered by the -q option.
The threshold option accepts the values "sensitive" and "selective" (predefined defaults in each classification module) and user defined thresholds as "cutoff=<cutoff_value>".
The module name is specified using the -m option and the jar filename of the prediction module (without the module folder name), e.g.:

java -jar TTSS_GUI-latest.jar -f test.fasta -m TTSS_ANIMAL-1.0.1.jar -t selective -o test.out -q

or

java -jar TTSS_GUI-latest.jar -f test.fasta -m TTSS_STD-latest.jar -t cutoff=0.995 -o test.out -q