Documentation for MutPred2 repository
- MATLAB R2017b or earlier (not tested on earlier versions)
- PSI-BLAST executable and associated files (bare-bones version included here but full version available here
- At least 4 GB RAM
- At least 7 GB disk space (code + data and model files)
Description of files and sub-directories
- mutpred2.m: the main MATLAB function that makes predictions (calls the different functions in all_functions).
- startup.m: contains code to include the all files in the repo in MATLAB path (edit file before using - change the path to the location of the MutPred2 repo).
- excluded_builtin_functions.txt: all MATLAB functions that are part of the Bioinformatics or Statistics toolboxes that cannot be included under MATLAB's licensing restrictions.
- all_functions - directory containing all helper functions called by mutpred2.m.
- blast-2.2.18 - legacy version of the PSI-BLAST executable that is compatible with MutPred2 (bin subdirectory) and data files associated with PSI-BLAST (data subdirectory).
If you use code from this repository, the web-server or the standalone executable in your work, please cite:
MutPred2: inferring the molecular and phenotypic impact of amino acid variants
Vikas Pejaver, Jorge Urresti, Jose Lugo-Martinez, Kymberleigh A. Pagel, Guan Ning Lin, Hyun-Jun Nam, Matthew Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac bioRxiv 134981; doi: https://doi.org/10.1101/134981
Data and code
- The code here corresponds to MutPred2.0, the version used for all analyses in the bioRxiv paper (and the main text of the published paper).
- There is currently no internal organization within the all_functions directory, as these needed to be placed in one location when compiling the standalone executable.
- If you are looking for MutPred2's training set, a subset of the training data for MutPred2 is available here.
- We cannot share MATLAB-related files or any of MATLAB's proprietary functionsand have excluded them to the best extent possible. However, please be aware of MATLAB's licensing restrictions when modifying and/or redistributing any code.
- Although MutPred2 requires an unsupported legacy version of PSI-BLAST, please refer to the BLAST suite's license before modifying and/or redistributing.