To extract the tool from the packed archive, which can be obtained from our download section, use the command: TFpredict can alternatively be used with a local installation of InterProScan. To support applications, which require the processing of a large number of sequences (e.g., the genome-wide prediction of TFs in a specific organism)
Thus, installing the perl stand-alone version of InterProScan (approx. The stand-alone version of TFpredict is equipped withĪ command-line interface which can be used for the batch processing of multiple protein sequences given in FASTA format.įor convenience, TFpredict uses the webservice version of InterproScan. Stand-alone version at our download section.
If you prefer to locally install your own copy of TFpredict, you can get the latest We recommend using theĪny installation and provides a user-friendy webinterface. TFpredict is available as a stand-alone version and as an online version.
If the tool is used in conjunction with SABINE the DNA motif of the TF may be determined in another prediction step.įor this purpose, TFpredict generates a machine-readable text file which can be post-processed using the tool SABINE to perform the inference of the The sequence regions spanned by DNA-binding domains are identified. In short, TFpredict combines sequence similarity searching with supervised machine learning methods (e.g., SVM, KNN, Naive Bayes)įor the identification of TFs and the prediction of their structural superclass.įurthermore, using the domain detection tool InterProScan in conjunction with a gene ontology-based filter Then we will click OK.The tool TFpredict provides an effective means for the identification and structural annotation of transcription factors (TFs),īased on sequence homology features inferred from their amino acid sequence using the tool Here we will set the Variable Name as JAVA_HOME and the Variable Value the path or Java, JRE or JDK which is C:\Program Files\Java\jdk-12 in this example. We click to the New in order to create a new system variable. Open Environment Variablesīelow we can see the environment variables menu where we will create the JAVA_HOME system variable and set the path accordingly. In the system properties, we will navigate to the Advanced tab which provides the Environment Variables button like below. We can also open it from the File Explorer -> Computer -> Right Click. We will open the computer properties with by running sysdm.cpl in the Run menu like below. We can set this path as Java HOME_PATH environment variable. Now we have learned the path of the Java, JRE or JDK installation. Locate JRE or JDK Path Set Java HOME_PATH Environment Variable Locate JRE or JDK PathĪnd under the Java directory the JDK is residing. JRE or JDK generally installed on the Program Files or Program Files(x86) directory under the Java directory like below. Locate JRE or JDK Pathīefore starting the configuration we have to locate the JRE or JDK path.
In this tutorial, we will learn how to set up Java, JRE, and JDK operating system path variables in order to work properly. JDK or Java Development Kit is used to develop Java applications. JRE or Java Runtime Environment is used to run Java application. Java is a very popular programming language which provides a different component in order to run, develop Java applications.