CRISPRloci: comprehensive and accurate annotation of CRISPR–Cas systems

Abstract

CRISPR–Cas systems are adaptive immune systems in prokaryotes, providing resistance against invading viruses and plasmids. The identification of CRISPR loci is currently a non-standardized, ambiguous process, requiring the manual combination of multiple tools, where existing tools detect only parts of the CRISPR-systems, and lack quality control, annotation and assessment capabilities of the detected CRISPR loci. Our CRISPRloci server provides the first resource for the prediction and assessment of all possible CRISPR loci. The server integrates a series of advanced Machine Learning tools within a seamless web interface featuring: (i) prediction of all CRISPR arrays in the correct orientation; (ii) definition of CRISPR leaders for each locus; and (iii) annotation of cas genes and their unambiguous classification. As a result, CRISPRloci is able to accurately determine the CRISPR array and associated information, such as: the Cas subtypes; cassette boundaries; accuracy of the repeat structure, orientation and leader sequence; virus-host interactions; self-targeting; as well as the annotation of cas genes, all of which have been missing from existing tools. This annotation is presented in an interactive interface, making it easy for scientists to gain an overview of the CRISPR system in their organism of interest. Predictions are also rendered in GFF format, enabling in-depth genome browser inspection. In summary, CRISPRloci constitutes a full suite for CRISPR–Cas system characterization that offers annotation quality previously available only after manual inspection.

Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains

“…The leading sequences often vary in size, ranging from tens to hundreds of bp, mostly upstream of the 5′ end of the first repeat, usually a non-coding sequence consisting of contiguous AT structures that are identified in the same species ( Alkhnbashi et al, 2021 ). It has also been suggested that the leader sequence may be the promoter for the transcription initiation of CRISPR arrays ( Marraffini, 2015 ).…”

CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection

“…The latter is suitable for large datasets. We plan to integrate CRISPRtracrRNA into the CRISPRloci ( Alkhnbashi et al , 2021 ) web server in order to provide users with a more in-depth CRISPR-Cas analysis.…”

Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation

“…To define new and extended Acr protein families, we performed an all-against-all sequence similarity comparison on the Acr protein sequences using the Fasta tool ( 48 ). Subsequently, we clustered the Acrs using the Markov Cluster Algorithm (MCL) ( 49 ) based on previously published similarity criteria ( 50 ). Next, we used the MUSCLE tool ( 51 ) to generate a multiple sequence alignment (MSA) for each protein cluster.…”