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bioRxiv · 10.64898/2026.05.15.725432

TAMIPAMI: Software and methods for PAM/TAM identification for CRISPR and OMEGA gene editing systems

Orosco, C.·Jain, P. K.·Rivers, A. R.
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Abstract

Protospacer adjacent motifs (PAMs) and target-adjacent motifs (TAMs) are essential for target recognition by CRISPR-Cas and TnpB nucleases. Here we present TAMIPAMI, an efficient experimental and computational framework for rapid PAM/TAM identification. TAMIPAMI requires only a single control library and Cas or TnpB-treated library, simplifying experimental design, reducing cost, and providing greater accessibility for users. The platform interprets sequencing data with interactive visualizations and introduces a novel algorithm that determines the minimal exact set of degenerate IUPAC sequences describing the observed PAM/TAM patterns. Using this approach, we accurately recovered canonical motifs for several nucleases, including SpCas9, LbCas12a, AsCas12a, BrCas12b, Cas12i1, and AmaTnpB. TAMIPAMI is available as both a web application and command-line tool, ultimately providing an accessible and efficient platform for PAM/TAM discovery and characterization across CRISPR and OMEGA systems.

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Orosco, C., Jain, P. K., Rivers, A. R.. 2026-05-16. TAMIPAMI: Software and methods for PAM/TAM identification for CRISPR and OMEGA gene editing systems. https://doi.org/10.64898/2026.05.15.725432

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