Spacer2PAM

Spacer2PAM predicts protospacer adjacent motif (PAM) sequences from CRISPR array spacers to identify functional PAMs required by endogenous CRISPR systems for genome editing applications.

Key Features:

• R package implementation: Implemented as an R package that analyzes CRISPR array spacers to predict potential protospacer adjacent motif (PAM) sequences.
• Quick Mode: Generates a single PAM prediction likely to be functional for rapid use.
• Comprehensive Mode: Creates targeted, unpooled PAM libraries of manageable size suitable for screening.
• Support for challenging organisms: Produces PAM predictions and library designs intended to reduce the need for randomized DNA library screening in slow-growing or difficult-to-transform organisms.
• Experimental validation: Predictions have been experimentally validated for the type I-B CRISPR system of Clostridium autoethanogenum, identifying seven functional PAM sequences that mediate interference.

Scientific Applications:

• Endogenous CRISPR system development: Enables identification of functional PAMs for deploying endogenous CRISPR systems in target organisms.
• Genetic engineering and strain development: Facilitates precise genome modifications for microbial strain engineering where heterologous CRISPR effectors are undesirable.
• Industrial biotechnology and synthetic biology: Supports applications in industrial biotechnology and synthetic biology by informing PAM choices for genome editing workflows.

Methodology:

Predicts potential PAM sequences from CRISPR array spacers and provides two computational modes: Quick Mode to output a single predicted functional PAM and Comprehensive Mode to generate designs for targeted, unpooled PAM libraries for screening.