Computational protocol: The orphan germinant receptor protein GerXAO (but not GerX3b) is essential for L-alanine induced germination in Clostridium botulinum Group II

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Protocol publication

[…] For identification of gerX genes in the genomes of C. botulinum Group II strains, genome sequences were re-annotated using Prokka version 1.12. Roary version 3.5.7 was used for comparative genomics. Alignments were made with Clustal omega and MEGA version 6.0 and used for generation of phylogenetic trees using the Neighbour Joining option. Figtree was used for annotation of phylogenetic trees. Conserved domains were identified using the Conserved Domain Database (NCBI). […]

Pipeline specifications

Software tools Prokka, Roary, Clustal Omega, FigTree
Databases CDD
Applications Genome annotation, Phylogenetics
Organisms Clostridium botulinum, Homo sapiens
Diseases Botulism
Chemicals Alanine