Datasets and Command Line version download

Universidad Complutense de Madrid - Inmunology Departament




Training and testing datasets
Training dataset
Download  
Testing dataset
Download


Version to run in Command Line

IMPORTANT: Command line version (ONLY predicts exosome protein secretion)

Main Python Script

Dependence Perl Script

Model
For model request write to parecheg@med.ucm.es

Software dependences
1) Weka (preferible weka 3.9.3)
2) Perl
3) Python (with os and argparse packages installed)

Installation instructions:

1) Download the main script, the dependence perl script and the model (request to parecheg@med.ucm.es).

2) Save all in the same directory.

3) Test sequences must be in FASTA format. It is recomendable to keep the fasta file in the same directory than the execution python script and model


Usage:

- Help page:
./exopred_comand_line -h
- Run software:

   -> Print output in terminal
./exopred_comand_line -f fasta_input_name -w weka_executable
   -> Save output
./exopred_comand_line -f fasta_input_name -w weka_executable -o 
output_name

Note:

  - The software creates temporarily files in the directory where is executed
  - All arguments recognize both absolute and relative pathways



Please cite:

Ras-Carmona, A., Gomez-Perosanz, M., & Reche, P. A. (2021). Prediction of unconventional protein secretion by exosomes. BMC bioinformatics, 22(1), 333. https://doi.org/10.1186/s12859-021-04219-z


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