CRISPRimmunity

Please upload a prokaryotic genome sequence file in FASTA or Multi-FASTA format or GenBank format (Just for sequences from the same genome if containing multiple contigs)

Upload a prokaryotic genome sequence file and set corresponding parameters

CRISPR-Cas detection and classification

Predict CRISPR array(s) using CRISPRCasFinder, CRT, PILER-CR and merge the CRISPR arrays;

Annotate cas proteins using hmmscan, and annotate other functional proteins nearby using rpsblast;

Identify repeat type using hmmscan;

Annotate CRISPR-Cas type according to cas gene content;

Self-targeting and MGE targeting detection

Detect self-targeting events and interactive bacteriophages through spacer-protospacer matching using BLASTN;

Prophage detection

Predict prophage region(s) using DBSCAN-SWA;

Anti-CRISPR protein detection

Detect known anti-CRISPR (Acr) gene, Acr-associated gene (Aca) and HTH domain

Check whether known Acrs are in the prophages with Self-targetings;

Return results for CRISPR-Cas system annotation, Acr and Aca gene annotation, HTH domain annotation, self-targeting spacer search, repeat type identification, bacteria-phage interaction detection, and prophage detection.

Parameter settings

CRISPR-Cas module

CRISPR array identification methods: CRISPRCasFinder CRT PILER-CR

The number of upstreamed or downstreamed proteins of the predicted CRISPR array to annotate, default:10

The neighbour range of the predicted CRISPR array to identify cas genes, default:20000bp

Self-targeting module

Mismatch for results of identifying self-targeting, default:2

Coverage(0~1) for results of identifying self-targeting, default:1

MGE targeting module

Mismatch for results of predicting interacting MGE, default:2

Coverage(0~1) for results of predicting interacting bacteriophages, default:0.9

Anti-CRISPR protein module

Predict known Acr, Aca and HTH domain

Identity for results of predicting known anti-CRISPR protein: 100%
Coverage for results of predicting known anti-CRISPR protein: 100%

Example 1: Predicted results for Staphylococcus schleiferi strain 5909-02, complete genome. One Type II CRISPR-Cas system was found with 16 spacers taregting prophages, plasmids and phages. Two AcrIIA13 proteins were detected in two prophages with protospacers, neighbored with an Aca.