The CRISPR-Cas systems not only play key roles in prokaryotic acquired immunity, but also can be adapted to powerful genome editing tools. Here, we developed CRISPRminer, a knowledge database and web-server to guide CRISPR-Cas associated studies, including CRISPR locus and Cas protein prediction, CRISPR-Cas systems classification, self-targeting detection, microbe-phage infection networks and anti-CRISPRs annotation.

1. “CRISPR-Cas” module: users can browse the pre-calculated CRISPR-Cas systems through taxonomy tree, or fuzzy search of the bacterial/archaeal name or Refseq ID to visualize the detailed information. 395 Cas families were collected from a recent study Makarova et al 2015 (Nat Rev Microbiol).

2. “Classification” module provides types and subtypes of the CRISPR/Cas systems based on Cas genes contents and distinctive gene architectures according to the most recent classification studies, refer to Makarova et al 2015 (Nat Rev Microbiol) and Shmakov et al 2017 (Nat Rev Microbiol).

3. “Self-targeting” module provides a tool for users to search for self-targeting spacers. ‘‘Self-targeting’’ is a phenomenon observed in the intracellular food-borne pathogen Listeria monocytogenes, which has been utilized as a genomic marker for screening CRISPR-Cas inhibitor genes (Rauch, B. J. et al 2017).

4. “Interaction” module provides insight into bacteria-phage or archaea-virus interactions, and collects clues for understanding the general principle of infection and resistance between microbe and phage.

5. “Anti-CRISPR” module provides the information of 23 families of anti-CRISPRs currently identified in the CRISPR-bearing organisms.

Please email: fanzhang@hit.edu.cn when you have any question or problem about using CRISPRminer

Please cite: Zhang, F. et al. CRISPRminer is a knowledge base for exploring CRISPR-Cas systems in microbe and phage interactions. Communications Biology 1, 180, doi:10.1038/s42003-018-0184-6 (2018).

Developers: Fan Zhang; Yongkui Lai; Shijia Zhao; Haibin Zhou;