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 (http://blast.ncbi.nlm.nih.gov/Blast.cgi). 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 (http://www.xbase.ac.uk/colibase/) and in GenBank, using the CRISPR Finder application at http://crispr.u-psud.fr/. The DNA strands carrying the protospacer nucleotides complementary to the corresponding spacer sequence in the crRNA were aligned using the WebLogo application at http://weblogo.berkeley.edu/logo.cgi/to 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