Cas protein search
WHAT IS CasPEDIA?
CasPEDIA, or the Cas Protein Effector Database of Information and Assessment, is an encyclopedia of Class 2 CRISPR systems, presented in wiki format. Wiki entries provide comprehensive descriptions of enzyme activities, structures and sequences, complete with a literature review covering each nuclease's discovery, experimental considerations and applications.
CasPEDIA introduces CasIDs, which organize Cas enzymes by their functional properties. Inspired by the ENZYME Classification (E.C.) system, CasID nomenclature is composed of three digits, described below, that concisely describe effector properties and enable rapid identification of appropriate enzymes for a researcher's use case. CasIDs can be used to navigate the website through direct search in the search bar and using our Tool Finder.
Please visit the FAQ section for directions on navigating CasPEDIA and information about becoming a curator. Additional details about CasPEDIA are available in our preprint. Individuals interested in learning CRISPR fundamentals are encouraged to read CRISPRpedia, created by The Innovative Genomics Institute.
Currently, in preprint
CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes
Adler, B. A.*, Trinidad, M. I.*, Bellieny-Rabelo, D., Zhang, E., Karp, H. M., Skopintsev, P., ... & Doudna, J. A. (2023). doi: 10.32942/X2C31F
* Authors contributed equally
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To demonstrate CasIDs, consider SpyCas9a, with a CasID of 1.1.1.
- The Nuclease Activity for this enzyme falls under category 1, implying it has blunt double-strand cis nuclease-activity, and no trans nuclease-activity.1.
- The Targeting Requirements for SpyCas9a fit category 1, meaning it requires a 3' protospacer-adjacent motif (PAM)
- Finally, the Guide RNA (gRNA) Design and Multiplexing properties for this enzyme fall under category 1, such that the native CRISPR array for SpyCas9a requires a CRISPR RNA (crRNA) for targeting + a trans-acting crRNA (tracrRNA) for multiplexing to the protein backbone of the effector + additional factors for processing the array into mature guides. SpyCas9a can also be engineered to utilize a minimal array containing different single-guide RNAs (sgRNAs), represented as a contiguous, all-in-one crRNA + tracrRNA sequence.2,3.