CRISPRTarget

By Ambarish Biswas, Joshua N. Gagnon, Stan J. J. Brouns, Peter C. Fineran, Chris M. Brown. RNA Biology, 2013

295 citations recorded by the source corpus.

The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs (http://bioanalysis.otago.ac.nz/CRISPRTarget). This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/904d98d1a2f886e892e9f648b9743553d82d5a9a

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Citations in the corpus

Computational approaches to predict bacteriophage–host relationships (2015, methodology): “…for longer sequences, we adapted the parameters of the search as suggested by the CRISPRTarget tool that identifies the target of CRISPR spacers (Biswas et al. 2013) (i.e. using the blastn-short task, a maximum expect value of 1; a gap opening penalty 10; a gap extension penalty 2; a mismatch…”
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements (2018, unknown): “Using CRISPRTarget (30) with the cutoff score of 20 by default and the 125 497 CRISPRdbcollected non-redundant spacers (31), a total number of 831 targets of CRISPR spacers are found in 340 ICEs, in which 272 spacers are distributed on 104 experimentally validated ICEs (Supplementary Table S5).”
NCBI prokaryotic genome annotation pipeline (2016, methodology): “For CRISPRs prediction and annotation PGAP uses a combination of the CRISPR recognition tool (CRT) (26) and PILER-CR (27).”