Welcome to TM-SmiRs!

TM‑SmiRs is an end‑to‑end Python package that allows screening microRNA sequences for binding accessibility and secondary structure. Specifically, TM-SmiRs, a 𝐓oehold 𝐌ediated 𝐒trand displacement 𝗺𝗶cro𝐑NA 𝐬creening package, was built with the objective of providing a unified toolkit to select clinically relevant humnan microRNA targets with optimal properties for hybridisation. The package may be used for both diagnostic and therapeutic contexts. 🍐🍐🍐

Key Features

• Thermodynamic analysis of input sequences

• Sequence level similarity metrics against a human and non-human RT-qPCR reference primer (hsa-miR-16-5p and cel-miR-39-3p respectively)

• Radar plots for intuitive visual overview of balanced features

• Projection of user-specified microRNAs into a precomputed PCA embeddings graph with all categorised human microRNAs

• Interactive plotly maps for exploring results visually

Getting Started

To get started with TM-SmiRs , refer to Overview for a summary of what the package entails. Installation will then guide you further into pip installation instructions, and Documentation finally provides a full list of list of available commands.

Credits

If using this package for your research, please cite our paper:

@article{shortcode,
    title={TM-SmiRs: An end-to-end structural microRNA screening package evaluating strand availability},
    author={Inga Van den Bossche, Ines Silva, Chaewon Park, Adam Creamer, Molly},
    journal={Nucleic Acids Research},
    volume={vol},
    number={no},
    pages={pg-pg},
    year={2025},
    doi={doi}
}

And if you find TM-SmiRs useful give it a star on GitHub! 🌟

Star