GRAMEP - Genome vaRiation Analysis from the Maximum Entropy Principle

GRAMEP is a powerful, Python-based tool designed for the precise identification of Single Nucleotide Polymorphisms (SNPs) within biological sequences. It goes beyond basic SNP identification, offering advanced functionalities including:

• Intersection analysis: Analyze mutations found in different variants to identify shared mutations.
• Classification model training: Train a classification model to predict the class of new sequences.

GRAMEP is accessible through a robust and intuitive Command-Line Interface (CLI). The primary command is gramep, with sub-commands for each action the application can perform.

For detailed information, access the documentation.

How to install

The use of pipx is recommended for installing GRAMEP:

pipx install gramep

Although this is only a recommendation, you can also install the project with the manager of your choice. For example, pip:

pip install gramep

Quick Guide

Identifying the most informative SNPs

To identify the most informative Single Nucleotide Polymorphisms (SNPs) using GRAMEP, you will utilize the get-mutations command. Below, you will find the basic usage of this command:

gramep get-mutations [OPTIONS]

For detailed information on available options and how to use them, simply enter the following command:

gramep get-mutations --help

This will provide you with comprehensive guidance on how to make the most of the get-mutations command, allowing you to efficiently analyze and extract valuable SNPs from your biological sequences.

Identifying Mutation Intersection Between Variants

To identify the intersection of mutations present in two or more variants of the same organism, you can utilize the `get-intersection`` command provided by GRAMEP. Below, we outline the basic usage of this command:

gramep get-intersection [OPTIONS]

This command allows you to analyze and find common mutations shared among multiple variant sequences. For detailed information on available options and how to make the most of the get-intersection command, simply use the --help flag:

gramep get-intersection --help

Classifying Biological Sequences

To classify biological sequences using GRAMEP, you can utilize the classify command. Here is the basic usage of this command:

gramep classify [OPTIONS]

This command allows you to perform sequence classification tasks with ease. For detailed information on available options and how to use them effectively, use the --help flag:

gramep classify --help

Predicting Biological Sequences

The predict command of GRAMEP is used to perform class predictions on new biological sequences after training a classification model. Below, you'll find the basic usage of this command:

gramep predict [OPTIONS]

This command allows you to leverage your trained classification model to predict the classes of new biological sequences. For detailed information on available options and how to use them effectively, utilize the --help flag:

gramep predict --help

Note: Models saved by classify depend on the scikit-learn version used to train them. Models trained with an earlier GRAMEP version are not supported by this release and must be retrained with gramep classify.

Citation

Pimenta-Zanon, M.H., Kashiwabara, A.Y., Vanzela, A.L.L. et al. GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs. BMC Bioinformatics 26, 66 (2025). https://doi.org/10.1186/s12859-025-06037-z

@article{PimentaZanon2025,
  title = {GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs},
  volume = {26},
  ISSN = {1471-2105},
  url = {http://dx.doi.org/10.1186/s12859-025-06037-z},
  DOI = {10.1186/s12859-025-06037-z},
  number = {1},
  journal = {BMC Bioinformatics},
  publisher = {Springer Science and Business Media LLC},
  author = {Pimenta-Zanon,  Matheus Henrique and Kashiwabara,  André Yoshiaki and Vanzela,  André Luís Laforga and Lopes,  Fabricio Martins},
  year = {2025},
  month = feb 
}

Acknowledgements

• This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001, the Fundação Araucária, Governo do Estado do Paraná/SETI (Grant number 035/2019, 138/2021 and NAPI - Bioinformática).