Getting Started with TFpredict
This section will guide you through the installation, setup, and first steps to using TFpredict.
How to get started
The stand-alone version of TFpredict is equipped with a command-line interface which can be used for the batch processing of multiple protein sequences given in FASTA format. For convenience, TFpredict uses the webservice version of InterproScan. Thus, installing the perl stand-alone version of InterProScan (approx. 40GB) is not required.
Installing TFpredict
Download the JAR file TFpredict_1.4 from https://github.com/draeger-lab/TFpredict/releases and also the example file test_seq.fasta.
You can also clone this repository and build a new snapshot release using the ant script shipped with this project by executing the following command in the dist folder:
ant -f tfpredict_build.xml
TFpredict is completely implemented in Java and provided as a runnable JAR file. All platforms (Windows, Mac, Linux) are supported provided that Java (22.0.1 or later) and BLAST (NCBI BLAST 2.15.0+ or later) is installed. You can download the latest version of BLAST from https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/.
To install TFpredict, make sure you have the following dependencies:
Java™ (JDK 22.0.1 or later)
BLAST (NCBI BLAST 2.15.0+ or later)
The analysis framework of TFpredict is entirely written in Java. Thus, it requires that Java Virtual Machine (JDK version 22.0.1 or newer) is installed on your system.
Installation and configuration of BLAST
Follow the instructions at the BLAST home-page for your operating system. For Unix, go to http://www.ncbi.nlm.nih.gov/books/NBK52640/ For Windows, see the instructions http://www.ncbi.nlm.nih.gov/books/NBK52637/.
Having BLAST successfully installed, it is necessary to pass the path to the executable to TFpredict. To this end, define the environment variable
BLAST_DIR
on your system to point to the installation directory of your copy of BLAST. This might be, for instance,
Path |
Operating System |
|
macOS |
|
Linux |
|
MS Windows |
Note that x.x.xxx stands for some arbitrary version number of BLAST and must be replaced as necessary.
So, the variable BLAST_DIR could be set to one of the above example folders. In the bash under MacOS you would, e.g., type
export BLAST_DIR=/usr/local/ncbi/blast/
or on Windows in Command Prompt you would use
set BLAST_DIR=C:\program~\NCBI\blast-x.x.xxx\
before executing TFpredict.
Next Steps
Now that you have TFpredict set up, explore the detailed How to Use TFpredict - The Manual!
If you encounter any issues or need further assistance, please refer to other sections of this documentation or feel free to create an issue on our GitHub repository.