RBPPred 2.0        Liu Lab at Huazhong University of Science and Technology


RBPPred2.0: an updated program for RNA-binding proteins prediction from sequence

RBPPred2.0 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.

RBPPred2.0 is available:

Training set: Testing sets:

Instructions of installation and and usage of RBPPred2.0

Once RBPPred2.0 program downloaded, you can follow the steps below to compile and use the package:

  1. Type "tar xzvf RBPPred2.0.tar.gz" to uncompress the package
  2. Download the formated nr70.tar.gz (5.41G) and nr90.tar.gz (9.69G) to "RBPPred2.0/source/DeepCNF_SS_v1.02_release/databases/NR_new" directory and unpack them using "tar xzvf nr70.tar.gz" and "tar xzvf nr90.tar.gz"
  3. Download the formated nr80.tar.gz (7.71G) to "RBPPred2.0/blastdb" directory and uncompress it using "tar xzvf nr80.tar.gz"
  4. Go to the RBPPred2.0 directory, and type "./INSTALL.sh" to compile the program
  5. Use the command "./RBPPred2.0.sh input_fasta num_threads" to predict. Here, "input_fasta" is the protein sequence file in the fasta format. num_threads is the number of CPUs to be used. A random directory with suffix of ".RBPPred2" will be generated for saving outputs, and the "query.result" file in it is the final prediction result for each prediction.

Programs related to RBPPred2.0


Contact us:
Any questions about RBPPred2.0, 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
2. Zhang, X. and S. Liu, RBPPred2.0: sequence-based prediction of RNA-binding proteins. submitted.