RBPPred        Liu Lab at Huazhong University of Science and Technology


RBPPred: a program for RNA-binding proteins prediction from sequence

Update news: We recently update RBPPred to iRBPPred. More information at here

RBPPred is a sequence-based RNA-Binding Proteins Predictor, which employs a comprehensive feature representation from the amino acid sequence based on support vector machine (SVM). More than one sequence in the fasta format can be submited to the program. The output file presents the prediction result with probability for each sequence.

RBPPred is available:

Training set: Testing sets:

Instructions of installation and and usage of RBPPred

Once RBPPred program downloaded, you can follow the steps below to compile and use the package:

  1. Type "tar xzvf RBPPred.tar.gz" to uncompress the package
  2. Type "cd RBPPred" to change the current directory
  3. Type "./INSTALL.sh" to compile the program
  4. Use the command "./RBPPred.sh input_fasta num_threads" to predict. Here, "input_fasta" is the protein sequence file in the fasta format. num_threads is a user defined number of CPUs to use. A random directory with suffix of ".RBPPred" will be generated for saving outputs, and the "query.result" file in it is the final prediction result for each prediction.

Programs related to RBPPred


Data sets updated

Some proteins which have RNAs in their crystal structures are removed from the negative sets in the above data sets.
A minimum version of RBPPred to test:
The minimum version of RBPPred.mini provided here is just for testing, the prediction results may be different from the original results by using the above RBPPred package. Users should download the above big version of RBPPred.tar.gz for scientific research and prediction.
Contact us:
Any questions about RBPPred, please email to liushiyong@gmail.com.

Reference:
1. Zhang, X. and S. Liu, RBPPred: predicting RNA-binding proteins from sequence using SVM. Bioinformatics, 2016. Published PubMed