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Documentation for MutPred2 repository

Requirements

  • 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).

Citation

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

Additional notes

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.

License

  • 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.

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Source code for MutPred2.0

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