CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes

Abstract

CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models

“…Notably, the newly published Casλ (pseudopositive) and Cas12n (pseudonegative) homologs were excluded during the training process. For the testing dataset, we utilized recently published sequences from the CasPEDIA database 29 , with duplicates eliminated with a sequence similarity less than 70% compared to the training dataset. This included several Casλ and Cas12n homologs.…”

“…After redundancy removal, the Cas12 homologs published in the CasPEDIA 29 database included 29 pseudopositives (Cas12a, Cas12c, Cas12h, Cas12i, CasΦ, Cas12m and Casλ homologs) and 98 pseudonegatives (Cas12b, Cas12d, Cas12e, Cas12k and Cas12n homologs), which served as the testing dataset.…”