Computational protocol: Target Motifs Affecting Natural Immunity by a Constitutive CRISPR Cas System in Escherichia coli

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Protocol publication

[…] For the identification of the E. coli CRISPR-4 protospacer adjacent motif (PAM), regions of non-CRISPR loci containing sequences with over 90% identity to spacers of CRISPR-Cas I-F systems of E. coli strains were searched with the BLASTN program run against the nr/nt database at the NCBI Website ( When protospacers of different origin where found for a single spacer, the sequence with higher identity was selected for the analysis. Spacers were detected in E. coli sequences available through the coliBASE Website ( and in GenBank, using the CRISPR Finder application at The DNA strands carrying the protospacer nucleotides complementary to the corresponding spacer sequence in the crRNA were aligned using the WebLogo application at obtain sequence logos . The ends of the protospacers were used as reference for alignments and no gaps were introduced. […]

Pipeline specifications

Software tools BLASTN, WebLogo
Databases coliBASE xBASE
Application Genome data visualization
Organisms Escherichia coli
Chemicals Nucleotides