Computational protocol: Asymmetric positioning of Cas1–2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system

Similar protocols

Protocol publication

[…] The lists comprising of type I-E and other type I (excluding type I-E) organisms were compiled from previous study (). Using IHF-α as a query, we initiated blastp () search against the genomes harbouring type I-E and other type I (non-type I-E) CRISPR systems. Hits were considered bonafide if the E-value is less than 0.005 and the alignment coverage with respect to the query is at least 60%. Based on these criteria, we estimated the distribution of IHF across the species. Since HU and IHF are structurally similar and also shares similarity at the sequence level (), we relied on the annotation to distinguish between the two. The multiple sequence alignment corresponding to the leader region for type I-E CRISPR system was obtained from the CRISPRleader database (). The conservation profile was generated using WebLogo 3 (). […]

Pipeline specifications

Software tools BLASTP, CRISPRleader, WebLogo
Applications Genome annotation, Genome data visualization
Organisms Escherichia coli