Computational protocol: Conservation of σ28-Dependent Non-Coding RNA Paralogs and Predicted σ54-Dependent Targets in Thermophilic Campylobacter Species

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Protocol publication

[…] Genome sequences were downloaded as FASTA files with contigs or complete genome sequences from the NCBI website (http://www.ncbi.nlm.nih.gov/genome/browse/). Alignments were made with ClustalX2 and MEGA v5.2 [, ]. Genomes were searched using BLAST and Artemis. Targets for CjNC1 and CjNC4 were predicted using TargetRNA [], via the website http://snowwhite.wellesley.edu/targetRNA/. The defaults settings were used, except for the target area which was set to go from -50 to +3 based on the annotated translational start. […]

Pipeline specifications

Software tools Clustal W, MEGA-V, TargetRNA
Application GWAS
Organisms Campylobacter jejuni, Escherichia coli
Diseases Ocular Motility Disorders