MobiDB-lite is a Python program designed to generate a consensus prediction of intrinsically disordered regions in proteins. The consensus is generated by measuring predictors agreement where at least 6/9 of predictors must agree to assign disorder state to a residue. A mathematical morphology (MM) dilation/erosion processing is applied to smooth the prediction and short regions are filtered out.
The code is integrated into the InterProScan software. The MobiDB-lite output is available in the MobiDB, InterPro, PDBe, PDBe-KB and UniProtKB databases.
This version of MobiDB has been developed in collaboration with Matthias Blum who optimized its execution time by 10 times. Matthias' version is available here (and called IDRPred).
MobiDB-lite is also available as Docker container MobiDB-lite_docker
MobiDB-lite 3.0: Fast consensus annotation of intrinsic disorder flavors in proteins
Necci M, Piovesan D, Clementel D, Dosztányi Z, Tosatto SCE
Bioinformatics (2020) - DOI: 10.1093/bioinformatics/btaa1045
You can use the tool simply cloning this repo and running __main__.py Python script.
which implements a command line interface.
To avoid import errors you need to add the source root folder
to the PYTHONPATH environment variable. For example:
export PYTHONPATH=/path/to/MobiDB-lite/src:$PYTHONPATH
Alternatively, you can install the package with Pip. No need to export any variable in this case.
From GitHub:
git clone https://github.com/BioComputingUP/MobiDB-lite.git
pip install .
In the case the calculation of ensemble properties (compactness), the nu parameter, the following optional dependencies are required:
- scikit-learn >= 1.4.2
- numba >= 0.59.1
The program can be executing the command line interface or as a library. Both the command line and the library accept the following positional arguments:
- input file - Protein sequences to be analyzed in FASTA format
- output file - The output file, different formats can be generated
When executed from the command line the script logs information about the calculation in the console (standard error) and
will create an output file containing the prediction results.
A different temporary folder can be specified using the --tempdir option.
The following options are available:
When installed with pip the script is available as mobidb_lite command.
mobidb_lite input_fasta_file output_file
If you simply cloned the repository:
python3 /path/to/MobiDB-lite/src/mobidb_lite/__main__.py input_fasta_file output_file