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Fig. 2 | BMC Genomics

Fig. 2

From: CRISPRDetect: A flexible algorithm to define CRISPR arrays

Fig. 2

CRISPRDetect predictions for E. coli K-12- text output. CRISPRDetect identifies two CRISPR arrays in a K-12 genome, corresponding to the well characterised CRISPR 2.1 and 2.3 loci. This genome is provided as one of the test sets at http://bioanalysis.otago.ac.nz/CRISPRDetect/. CRISPRDetect output. E. coli arrays - both arrays are reverse-complemented in the CRISPRDetect prediction (based on matches to reference repeat and other features by CRISPRDirection) a CRISPR 2.1 The array section of the CRISPRDetect output is shown, showing base differences e.g. a. TT mutations in the repeat toward the predicted 3’ end. b. The full output is shown, and specific features are in bold. For CRISPR 2.3 the reference repeat match also permitted inclusion of the experimentally verified last base (G) in the repeat, although it varies in two of six repeats (the first and last, bold). The score is high (8.14) and the components are shown below. The Directional analysis gives a ‘HIGH’ confidence for the reverse orientation as shown. The cas genes identified in the ‘.gbk’ file are listed as are the signature genes for any family present (only I-E in this example). c. CRISPRFinder prediction for E. coli CRISPR 2.3 for comparison. Prediction obtained from CRISPRdb predicted by CRISPRFinder

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