TAMIPAMI: Software and methods for PAM/TAM identification in CRISPR and OMEGA gene editing systems
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.
Read the paper
Related studies
- eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
- Online Survival Analysis Software to Assess the Prognostic Value of Biomarkers Using Transcriptomic Data in Non-Small-Cell Lung Cancer
- OptiType: precision HLA typing from next-generation sequencing data
- Nicotinic Cholinergic System and COVID-19: In Silico Identification of an Interaction between SARS-CoV-2 and Nicotinic Receptors with Potential Therapeutic Targeting Implications
- Saccharomyces cerevisiae cells have three Omega class glutathione S-transferases acting as 1-Cys thiol transferases
- Hemolysis at low blood flow rates: in-vitro and in-silico evaluation of a centrifugal blood pump
Go deeper in Evidence Hub
Evidence Hub adds a study data sheet (design, sample size, evidence level, key numbers), an AI summary and a chat grounded in the paper's text.