Computational protocol: Evaluation of conventional and response surface level optimisation of n-dodecane (n-C12) mineralisation by psychrotolerant strains isolated from pristine soil at Southern Victoria Island, Antarctica

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Protocol publication

[…] The 16S rRNA gene sequences of each purified strain were identified using BLASTn []. The alignment of the sequences was used for analysis under the neighbor-joining method [] fitting to the distances of Jukes-Cantor model []. Phylogenetic tree was constructed using PHYLIP software v3.696 [J. Q. Felsenstein, PHYLIP—phylogeny inference package, version 3.696] (http://evolution.genetics.washington.edu/phylip.html). Bacillus anthracis strain ATCC 14578 and E. coli strain U5/41 were used as the outgroups in the cladogram for ADL15 and ADL36, respectively. The evolutionary distance along with the robustness of the inferred trees was calculated and evaluated by neighbor-joining method by 1000 bootstraps replicates []. The constructed tree was viewed using the TreeView v3.0 software. […]

Pipeline specifications

Software tools BLASTN, PHYLIP, TreeViewX
Application Phylogenetics
Organisms Bacteria
Chemicals Carbon, Hydrocarbons, Sodium Chloride