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Releasing the BMS Tools: Expanding the Reach of Broad Mutational Scanning
Oct 28, 2025
Broad Mutational Scanning sits at the center of modern protein engineering, yet practical tools to support it are still limited. Our aim is to change that, by releasing code that others can use, adapt, and extend for their own high-throughput assays, we hope to push biology at scale forward.
Broad Mutational Scanning (BMS) has transformed how we explore sequence–function relationships, but practical tools for large-scale analysis remain scarce. While many labs perform variants of BMS, few have access to fully developed, open-source platforms that span design, screening, and analysis.
Today we’re highlighting one such platform, a complete pipeline developed and tested in the Plesa Lab, so others can build on it, extend it, and adapt it to their own systems.
Explore the repository on GitHub
This code provides a foundation for designing and analyzing mutational libraries using high-throughput sequencing data. It includes examples for processing variant counts, calculating fitness scores, and visualizing landscapes across thousands of homologs.
Our goal is simple: to enable the broader community to develop new, assay-specific pipelines tuned to the expanding variety of high-throughput screening methods. BMS is still early, and its full power depends on a broader proliferation of tools that can translate experimental data into exceptional insights and discovery.
Our team will continue developing additional resources to push these capabilities further. We look forward to seeing how others use, modify, and advance this foundation.
If you build something new on top of this work, we’d love to hear from you…and we’ll feature selected projects that extend the reach of BMS.
Repository: https://github.com/PlesaLab/DHFR
